bluuebunny/crossref_metadata_2025 huggingface dataset:
A new method and application of PacBio sequencing for low copy and difficulty preparation plasmids
Authors: Ma Xiaoshu , Wang Yusha , Jia Ruikai , Ye Hua
Published: May 2024

The Single Molecule Real Time (SMRT) system developed by Pacific Biosciences applies the principle of synthesis while sequencing and uses the SMRT chip as the sequencing carrier. The high starting amount and good integrity of DNA required by PacBio library construction has always been a headache. Generally, the total loading volume of PacBio sequencing is 10μg, and the concentration is not less than 200ng/μL, which is a huge challenge for low-copy plasmids. Tight plasmid means that when the bacterial chromosome replicates once, the plasmid replicates once, and each bacterium only contains 1 to 2 plasmids. The replicon of the plasmid determines the copy number of the plasmid. Low copy plasmids should produce 0.2-1 μg DNA per ml of LB culture. Low-copy plasmids play a key role in gene synthesis. When vectors are used for expression or other purposes, low-copy plasmids are used to reduce resource consumption caused by plasmid expansion. Low-copy plasmids are also used when plasmids have lethal gene clones. In order to solve the problem of low copy plasmid library database construction in PacBio, we used Phi29 polymerase to perform multiple substitution amplification of low copy plasmid, so as to obtain a large number of high molecular weight DNA to meet the computer requirements of PacBio. In addition, this study also established a PacBio sequencing method for bacterial fluids without the need for plasmid extraction steps, thereby reducing time and money costs.
FAPM: Functional Annotation of Proteins using Multi-Modal Models Beyond Structural Modeling
Authors: Xiang Wenkai , Xiong Zhaoping , Chen Huan , Xiong Jiacheng , Zhang Wei , Fu Zunyun , Zheng Mingyue , Liu Bing , Shi Qian
Published: May 2024

Assigning accurate property labels to proteins, like functional terms and catalytic activity, is challenging, especially for proteins without homologs and “tail labels” with few known examples. Unlike previous methods that mainly focused on protein sequence features, we use a pretrained large natural language model to understand the semantic meaning of protein labels. Specifically, we introduce FAPM, a contrastive multi-modal model that links natural language with protein sequence language. This model combines a pretrained protein sequence model with a pretrained large language model to generate labels, such as Gene Ontology (GO) functional terms and catalytic activity predictions, in natural language. Our results show that FAPM excels in understanding protein properties, outperforming models based solely on protein sequences or structures. It achieves state-of-the-art performance on public benchmarks and in-house experimentally annotated phage proteins, which often have few known homologs. Additionally, FAPM’s flexibility allows it to incorporate extra text prompts, like taxonomy information, enhancing both its predictive performance and explainability. This novel approach offers a promising alternative to current methods that rely on multiple sequence alignment for protein annotation. The online demo is at:https://huggingface.co/spaces/wenkai/FAPM_demo.
Microfluidic-enabled production of DNA barcoded APC library (MEDAL) for high throughput T cell epitope screening
Authors: Cui Xu , Liu Yi , Cheow Lih Feng
Published: May 2024

Screening for peptide fragments that can be displayed on antigen-presenting cells is an essential step in vaccine development. The current approach for this process is slow and costly as it involves separately pulsing cells with chemically synthesized peptides. We present Microfluidic-Enabled production of DNA-barcoded APC Library (MEDAL), a high throughput microfluidic droplet platform for parallel production of DNA-barcoded APCs loaded with enzymatically synthesized peptides. Droplets containing peptides and their encoding DNA are produced from microfluidic PCR-IVTT reaction. APCs presenting both peptides and DNA barcodes are obtained by injecting cells into these droplets. Up to 9,000 different APCs can be produced and screened within a 10-hour workflow. This approach allowed us to identify peptide sequences that bind to APCs expressing H-2Kb MHC class 1 molecule with next-generation sequencing of DNA barcodes.
Spectral Cluster Supertree: fast and statistically robust merging of rooted phylogenetic trees
Authors: McArthur Robert N. , Zehmakan Ahad N. , Charleston Michael A. , Huttley Gavin
Published: May 2024

Abstract

The algorithms for phylogenetic reconstruction are central to computational molecular evolution. The relentless pace of data acquisition has exposed their poor scalability and the conclusion that the conventional application of these methods is impractical and not justifiable from an energy usage perspective. Furthermore, the drive to improve the statistical performance of phylogenetic methods produces increasingly parameter-rich models of sequence evolution, which worsens the computational performance. Established theoretical and algorithmic results identify supertree methods as critical to divide-and-conquer strategies for improving scalability of phylogenetic reconstruction. Of particular importance is the ability to explicitly accommodating rooted topologies. These can arise from the more biologically plausible non-stationary models of sequence evolution.

We make a contribution to addressing this challenge with Spectral Cluster Supertree, a novel supertree method for merging a set of overlapping rooted phylogenetic trees. It offers significant improvements over Min-Cut supertree and previous state-of-the-art methods in terms of both time complexity and overall topological accuracy, particularly for problems of large size. We perform comparisons against Min-Cut supertree and Bad Clade Deletion. Leveraging two tree topology distance metrics, we demonstrate that while Bad Clade Deletion generates more correct clades in its resulting supertree, Spectral Cluster Supertree’s generated tree is generally more topologically close to the true model tree. Over large datasets containing 10000 taxa and -500 source trees, where Bad Clade Deletion usually takes -2 hours to run, our method generates a supertree in on average 20 seconds. Spectral Cluster Supertree is released under an open source license and is available on the python package index assc-supertree.

This research was undertaken with the assistance of resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government.
Microbiome Modulation Uncouples Efficacy and Toxicity Induced by Programmed Death-1/Programmed Death-Ligand1 Blockade
Authors: Cogrossi Laura Lucia , Zordan Paola , Grioni Matteo , Tosi Anna , Rizzo Nathalie , Policastro Anna , Mattorre Benedetta , Lorenzoni Marco , Meregalli Greta , Sisti Sofia , Sanvito Francesca , Chesi Marta , Bergsagel Leif , Clementi Nicola , Rosato Antonio , Bellone Matteo
Published: May 2024

While asymptomatic smoldering multiple myeloma (SMM) holds an overall risk of progression to multiple myeloma (MM) at 10% per year, only active surveillance is offered to most patients affected by SMM, which leaves them in anxiety and frustration. Intestinal microbiota and gut-born T helper 17 (Th17) lymphocytes may act as drivers of MM evolution. In transgenic Vk*MYC mice developingde novoMM, which invariably evolves from Early-MM that mimics SMM to full-blown Late-MM, we investigated the impact of gut microbiota modulation on disease progression and susceptibility to immune checkpoint blockade (ICB). We report that administering the human commensalPrevotella melaninogenicato mice affected by Early-MM significantly delayed evolution to Late-MM. Mechanistically, treatment withP. melaninogenicainduced increased production of short chain fatty acids. Butyrate prevented skew of dendritic cells towards a pro-Th17 phenotype and treated mice accumulated less disease induced Th17 cells in their bone marrow.P. melaninogenicaalso synergized with anti-PD-L1 antibodies by restraining Th17 cell expansion while unleashing ICB-induced full effector CD8+T cells, eventually blocking progression to full-blown disease. Similar results were obtained in mice challenged with bortezomib-resistant Vk*MYC tumor cells, a model of more aggressive MM. When mice were exposed to imiquimod to mimic ICB-associated psoriasis-like lesions,P. melaninogenicaameliorated skin lesions caused by ICB. Thus, modulation of the gut microbiota withP. melaninogenicamight represent a treatment for patients affected by SMM and would allow fully exploiting the antitumor potential of ICB in plasma cell dyscrasias.

Key points

Administration of the human commensalPrevotella melaninogenicato Vk*MYC mice delayed evolution to symptomatic multiple myeloma;

P. melaninogenicatherapeutically synergized with PD-1/PD-L1 blockade also limiting immune-related adverse events.
Human umbilical mesenchymal stem cell-derived mitochondria ameliorate maternal phenotype by improving placental mitochondria and vascular function in angiotensin II-induced preeclampsia rat
Authors: Cui Hui Xing , Liu Jun Xian , Kang Young Cheol , Han Kyuboem , Lee Hong Kyu , Kim Chun-Hyung , Zhang Yin Hua
Published: May 2024

Background

Mitochondrial transplantation (Mito-T) is a novel therapeutic strategy targeting ischemic cardiovascular diseases. Here, we tested the efficacy of human umbilical mesenchymal stem cell-derived mitochondria transplantation (Mito-T) on a rat model of PE.

Methods

PE was induced by infusing angiotensin II (Ang II) to SD pregnancy rats on gestation day 8 (GD 8). Mito-T (100 μg/μl) was injectedviajugular vein on GD 14.

Findings

On GD 20, PE rats showed high blood pressure, kidney and placental vascular abnormalities, reduced placental and fetal weights. Injected Mito-T was distributed intensively in the kidney, uterus and placenta of PE rats. Importantly, Mito-T reversed clinical manifestations of PE, restored placental abnormalities and reduced serum sFLT-1 levels and sFLT-1/PlGF ratio. In the placental mitochondria, Mito-T increased ETC complexes (complex I-V), improved mitochondrial membrane potential, ATP synthase and citrate synthase activities and biogenesis markers (PGC-1α, TFAM, NRF1) and reduced ROS production. Mito-T increased mitochondrial fusion proteins (OPA1, MFN1 and MFN2), reduced mitochondrial fission proteins (DRP1 and FIS1) and mitophagy proteins (PINK, BNIP3, BNIP3L, FUNDC1), restored sFLT-1 regulating calcineurin-NFAT-dependent pathways in the placental tissue, primary trophoblast cells and Bewo cell line. Furthermore, eNOS, nNOS and AT2R mRNA and protein expressions were restored in placenta and trophoblast cells after Mito-T.

Interpretation

This is the first study of PE treatment with Mito-T. Mito-T reverses pathological phenotypes of PE rats by improving placental mitochondrial and vascular function. The results provide proofs of concept of Mito-T as a potential therapeutic strategy for reducing maternal and fetal risks in PE patients.

Funding

This work is supported by Korean National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2019R1A2C1005720, NRF-2023R1A2C1005720), BK21 FOUR education program, Korean Society of Hypertension (Grant number KSH-R-2020), National Natural Science Foundation of China (NSFC 31660284, NSFC31860288).
Origins and diversity of pan-isotype human bone marrow plasma cells
Authors: Pacheco Gaspar A. , Rao Vishal , Yoo Duck Kyun , Saghaei Shahab , Tong Pei , Kumar Sachin , Marini-Rapoport Orlee , Allahyari Zahra , Moghaddam Ali S. , Esbati Romina , Alirezaee Aida , Parnes Aric , Patil Sarita U. , Wesemann Duane R.
Published: May 2024

Bone marrow plasma cells (BMPCs) produce durable, protective IgM, IgG, and IgA antibodies, and in some cases, pro-allergic IgE antibodies, but their properties and sources are unclear. We charted single BMPC transcriptional and clonal heterogeneity in food-allergic and non-allergic individuals across CD19 protein expression given its inverse correlation to BMPC longevity. Transcriptional and clonal diversity revealed distinct functional profiles. Additionally, distribution of somatic hypermutation and intraclonal antibody sequence variance suggest that CD19low and CD19high BMPCs arise from recalled memory and germinal center B cells, respectively. Most IgE BMPCs were from peanut-allergic individuals; two out of 32 from independent donors bound peanut antigens in vitro and in vivo. These findings shed light on BMPC origins and highlight the bone marrow as a source of pathogenic IgE in peanut allergy.
Genome assembly of the southern pine beetle (Dendroctonus frontalisZimmerman) reveals the origins of gene content reduction inDendroctonus
Authors: Copeland Megan , Landa Shelby , Owoyemi Adekola , Jonika Michelle M. , Alfieri Jamie , Sylvester Terrence , Hoover Zachary , Hjelmen Carl E. , Johnston J. Spencer , Kyre Bethany R. , Rieske Lynne K. , Blackmon Heath , Casola Claudio
Published: May 2024

Dendroctonus frontalis, also known as southern pine beetle (SPB), represents the most damaging forest pest in the southeastern United States. Strategies to predict, monitor and suppress SPB outbreaks have had limited success. Genomic data are critical to inform on pest biology and to identify molecular targets to develop improved management approaches. Here, we produced a chromosome-level genome assembly of SPB using long-read sequencing data. Synteny analyses confirmed the conservation of the core coleopteran Stevens elements and validated thebona fideSPB X chromosome. Transcriptomic data were used to obtain 39,588 transcripts corresponding to 13,354 putative protein-coding loci. Comparative analyses of gene content across 14 beetle and 3 other insects revealed several losses of conserved genes in theDendroctonusclade and gene gains in SPB andDendroctonusthat were enriched for loci encoding membrane proteins and extracellular matrix proteins. While lineage-specific gene losses contributed to the gene content reduction observed inDendroctonus, we also showed that widespread misannotation of transposable elements represents a major cause of the apparent gene expansion in several non-Dendroctonusspecies. Our findings uncovered distinctive features of the SPB gene complement and disentangled the role of biological and annotation-related factors contributing to gene content variation across beetles.
Recovery mode: Marine protected areas enhance the resilience of kelp species from marine heatwaves
Authors: Olguín-Jacobson Carolina , Arafeh-Dalmau Nur , Early-Capistrán Michelle-María , Montes José Antonio Espinoza , Hernández-Velasco Arturo , Martínez Ramón , Romero Alfonso , Torre Jorge , Woodson C. Brock , Micheli Fiorenza
Published: May 2024

Marine protected areas (MPAs) can promote population recovery from climate change impacts by reducing local stressors, such as fishing. However, with extreme climatic events such as marine heatwaves (MHWs) increasing in frequency and duration, it remains unclear whether MPAs enhance recovery following these acute perturbations, and how recovery varies across species and ecological traits (e.g., sedentary vs mobile species). We used 16 years (2007-2022) of kelp forest monitoring data in Isla Natividad, Baja California Sur, Mexico, to assess the impact of the 2014-2016 MHWs on fish and invertebrate communities. Then we evaluated the impact and recovery from the MHWs of economically and ecologically important invertebrate species inside and outside two fully protected marine reserves. We found that the 2014-2016 MHWs, which were the most intense and persistent ever observed in Isla Natividad, impacted invertebrates but not fish biomass. Marine reserves did not confer resistance to the MHWs, however, reserves did enhance the recovery of some species after the MHWs. Inside marine reserves, abalone (Haliotisspp.) and wavy turban snail (Megastraeaspp.) (benthic sedentary invertebrates) recovered to pre-heatwave biomass after two years and spiny lobster (Panulirus interruptus) (benthic mobile invertebrate) after four years. Outside the reserves, abalone recovered after three years, while the other two species never recovered. The warty sea cucumber (Apostichopus parvimensis) population collapsed after the MHWs and never recovered inside nor outside the reserve. Remarkably, abalone biomass had an outstanding and sustained recovery inside reserves, with a 5.6-fold increase in biomass after the MHWs, which was over three times higher than the recovery reported outside the reserve. Our analysis of long-term monitoring data shows that marine reserves cannot prevent adverse impacts from extreme climatic events but can enhance species recovery following these events. Benefits conferred by marine reserves, however, are species-specific and may be limited to species with limited dispersal and localized population dynamics.
Investigating spatial dynamics in spatial omics data with StarTrail
Authors: Chen Jiawen , Xiong Caiwei , Sun Quan , Wang Geoffery W. , Gupta Gaorav P , Halder Aritra , Li Yun , Li Didong
Published: May 2024

Spatial omics technologies revolutionize our view of biological processes within tissues. However, existing methods fail to capture localized, sharp changes characteristic of critical events (e.g. tumor development). Here, we present StarTrail, a novel gradient based method that powerfully defines rapidly changing regions and detects "cliff genes", genes exhibiting drastic expression changes at highly localized or disjoint boundaries. StarTrail, the first to leverage spatial gradients for spatial omics data, also quantifies directional dynamics. Across multiple datasets, StarTrail accurately delineates boundaries (e.g., brain layers, tumor-immune boundaries), and detects cliff genes that may regulate molecular crosstalk at these biologically relevant boundaries but are missed by existing methods. For instance, StarTrail precisely pinpointed the cancer-immune interface in a HER2+ breast cancer dataset, unveiled key cliff genes including a potential prognostic biomarker IGSF3, highlighting NK-, B-cell mediated immunity, and B cell receptor signaling pathways missed by all spatial variable gene methods attempted. StarTrail, filling important gaps in current literature, enables deeper insights into tissue spatial architecture.
Direct inference of the distribution of fitness effects of spontaneous mutations from recombinant inbredC. elegansmutation accumulation lines
Authors: Crombie Timothy A. , Rajaei Moein , Saxena Ayush S. , Johnson Lindsay M. , Saber Sayran , Tanny Robyn E. , Ponciano José Miguel , Andersen Erik C. , Zhou Juannan , Baer Charles F.
Published: May 2024

The distribution of fitness effects (DFE) of new mutations plays a central role in evolutionary biology. Estimates of the DFE from experimental Mutation Accumulation (MA) lines are compromised by the complete linkage disequilibrium (LD) between mutations in different lines. To reduce LD, we constructed two sets of recombinant inbred lines from a cross of twoC. elegansMA lines. One set of lines (“RIAILs”) was intercrossed for ten generations prior to ten generations of selfing; the second set of lines (“RILs”) omitted the intercrossing. Residual LD in the RIAILs is much less than in the RILs, which affects the inferred DFE when the sets of lines are analyzed separately. The best-fit model estimated from all lines (RIAILs + RILs) infers a large fraction of mutations with positive effects (∼40%); models that constrain mutations to have negative effects fit much worse. The conclusion is the same using only the RILs. For the RIAILs, however, models that constrain mutations to have negative effects fit nearly as well as models that allow positive effects. When mutations in high LD are pooled into haplotypes, the inferred DFE becomes increasingly negative-skewed and leptokurtic. We conclude that the conventional wisdom - most mutations have effects near zero, a handful of mutations have effects that are substantially negative and mutations with positive effects are very rare – is likely correct, and that unless it can be shown otherwise, estimates of the DFE that infer a substantial fraction of mutations with positive effects are likely confounded by LD.
Microbial network inference for longitudinal microbiome studies with LUPINE
Authors: Kodikara Saritha , Lê Cao Kim-Anh
Published: May 2024

The microbiome is a complex ecosystem of interdependent taxa that has traditionally been studied through cross-sectional studies. However, longitudinal microbiome studies are becoming increasingly popular. These studies enable researchers to infer taxa associations towards the understanding of coexistence, competition, and collaboration between microbes across time. Traditional metrics for association analysis, such as correlation, are limited due to the data characteristics of microbiome data (sparse, compositional, multivariate). Several network inference methods have been proposed, but have been largely unexplored in a longitudinal setting.

We introduce LUPINE (LongitUdinal modelling with Partial least squares regression for NEtwork inference), a novel approach that leverages on conditional independence and low-dimensional data representation. This method is specifically designed to handle scenarios with small sample sizes and small number of time points. LUPINE is the first method of its kind to infer microbial networks across time, while considering information from all past time points and is thus able to capture dynamic microbial interactions that evolve over time. We validate LUPINE and its variant, LUPINE single (for single time point analysis) in simulated data and four case studies, where we highlight LUPINE’s ability to identify relevant taxa in each study context, across different experimental designs (mouse and human studies, with or without interventions, as short or long time courses). We propose different metrics to compare the inferred networks and detect changes in the networks across time, groups or in response to external disturbances.

LUPINE is a simple yet innovative network inference methodology that is suitable for, but not limited to, analysing longitudinal microbiome data. The R code and data are publicly available for readers interested in applying these new methods to their studies.
Olive phenolic compounds, potent tankyrase 1 inhibitor exhibit anti colon cancer effects by blocking Wnt/β-catenin pathway
Authors: Sain Arindam , Barman Soumen , Khamrai Dipsikha , Srinivas M , Singh Prerna , Simpi Bhargav , Varshney Mayuri , Naskar Debdut
Published: May 2024

Colon cancer (CC) needs special attention to develop novel targets and therapeutic approaches, as the total number of morbidity and mortality is growing rapidly. Although Olive has been long reported for its anti-CC activities but the mode is not completely understood yet. Here, we targeted tankysare 1 (TNKS), an important mediator of the Wnt/β-catenin pathway, crucial in colon carcinogenesis. Bioinformatics analysis revealed that the mutation and copy number alterations ofTNKSis found to be 12% whereas the proteins expression ofTNKSis moderate to high in tumor groups vs normal in CC datasets. On the more,TNKSand its positively associated genes are found to be concomitant with several carcinogenesis related biological processes and signaling pathways. Further, three olive phytochemicals (apigenin, luteolin, and quercetin), which were shortlisted by employing filters like drug likeness and toxicity screening, molecular docking and finally molecular dynamics simulations, can target tankyrase 1. These ployphenols demonstrated cytotoxic effect in CC (HT-29) cells either alone or in combination. Further, these compounds successfully reduced β-catenin level and its target genes (CCND1, CDK4, andMYC). Overall, inhibition of the Wnt/β-catenin pathway by targeting tankyrase 1 was revealed as one of the anti-CC mechanisms of olive polyphenols.
The potential impacts of vector host species fidelity on zoonotic arbovirus transmission
Authors: Sulaimon Tijani A. , Wood Anthony J. , Bonsall Michael B. , Boots Michael , Lord Jennifer S.
Published: May 2024

The interaction between vector host preference and host availability on vector blood feeding behaviour has important implications for the transmission of vector-borne pathogens. In particular in multi-host disease systems the fidelity of the vector biting behaviour has the potential to have important implications to disease outcomes, particularly when there are amplifying and dead-end hosts. Using a mathematical model we showed that vector fidelity to the host species they take a first blood meal from leads to non-homogeneous mixing between hosts and vectors. Taking Japanese encephalitis virus (JEV) as a case study, we investigated how vector preference for amplifying vs dead-end hosts and fidelity can influence JEV transmission. We show that in regions where pigs (amplifying hosts) are scarce compared to cattle (dead-end hosts preferred by common JEV vectors), JEV can still be maintained through vector fidelity. Our findings demonstrate the importance of considering fidelity as a potential driver of transmission, particularly in scenarios such as Bangladesh and India where the composition of the host community might initially suggest that transmission is not possible.
wgbstools: A computational suite for DNA methylation sequencing data representation, visualization, and analysis
Authors: Loyfer Netanel , Rosenski Jonathan , Kaplan Tommy
Published: May 2024

Next-generation methylation-aware sequencing of DNA sheds light on the fundamental role of methylation in cellular function in health and disease. These data are commonly represented at a single CpG resolution, while single-molecule fragment-level analysis is often overlooked.

Here, we presentwgbstools, an extensive computational suite tailored for methylation sequencing data. wgbstools allows fast access and ultra-compact anonymized representation of high-throughput methylome data, obtained through various library preparation and sequencing methods. Additionally,wgbstoolscontains state-of-the-art algorithms for genomic segmentation, biomarker identification, genetic and epigenetic data integration, and more. wgbstools offers fragment-level analysis and informative visualizations, across multiple genomic regions and samples.
Resolving sulfation PTMs on a plant peptide hormone using nanopore sequencing
Authors: Chen Xiuqi , van de Sande Jasper W. , Ritmejeris Justas , Wen Chenyu , Brinkerhoff Henry , Laszlo Andrew H. , Albada Bauke , Dekker Cees
Published: May 2024

Peptide phytohormones are decorated with post-translational modifications (PTMs) that are crucial for receptor recognition. Tyrosine sulfation on these hormones is essential for plant growth and development1. Measuring the occurrence and position of sulfotyrosine is, however, compromised by major technical challenges during isolation and detection2. We recently introduced a nanopore peptide sequencing method that sensitively detects PTMs at the single-molecule level3. By translocating PTM variants of the plant pentapeptide hormone phytosulfokine (PSK) through a nanopore, we here demonstrate accurate identification of sulfation and phosphorylation on the two tyrosine residues of PSK. Sulfation can be clearly detected and distinguished (>90%) from phosphorylation on the same residue. Moreover, the presence or absence of PTMs on the two close-by tyrosine residues can be accurately determined (>96% accuracy). Our findings demonstrate the extraordinary sensitivity of nanopore protein measurements, providing a new tool for identifying sulfation on peptide phytohormones and promising wider applications to identify protein PTMs.
TITINdb2 – Expanding Annotation and Structural Information for Protein Variants in the Giant Sarcomeric Protein Titin
Authors: Weston T. , Ng J. C-F. , Gracia Carmona O. , Gautel M. , Fraternali F.
Published: May 2024

Structured Abstract

We present TITINdb2, an update to the TITINdb database previously constructed to facilitate the identification of pathogenic missense variants in the giant protein titin, which are associated with a variety of skeletal and cardiac myopathies. The database and web portal have been substantially revised and include the following new features: (i) an increase in computational annotation from 4 to 20 variant impact predictors, available through a new custom data table dialogue; (ii) thorough structural coverage of single domains with AlphaFold2 predicted models; (iii) newly predicted domain-domain interface annotations; (iv) an expandedin silicosaturation mutagenesis incorporating 4 variant impact predictors; (v) a comprehensive overhaul of available data, including population data sources and variants reported pathogenic in the literature; (vi) A curated mapping of existing protein, transcript and chromosomal sequence positions and a new variant conversion tool to translate variants in one format to any other format.

Availability and Implementation

Database accessible via titindb.kcl.ac.uk/TITINdb/

Contact

Franca Fraternali (f.fraternali@ucl.ac.uk)

Supplementary Information

Available
Proteins with proximal-distal asymmetries in axoneme localisation control flagellum beat frequency
Authors: Fort Cecile , Walker Benjamin J. , Baert Lore , Wheeler Richard John
Published: May 2024

The 9+2 microtubule-based axoneme within motile flagella is well known for its symmetry. However, examples of asymmetric structures and proteins asymmetrically positioned within the 9+2 axoneme architecture have been identified in multiple different organisms, particularly involving the inner or outer dynein arms, with a range of functions. Here, mapped, genome-wide, conserved proximal-distal asymmetries in the uniflagellate trypanosomatid eukaryotic parasites. Building on the genome-wide localisation screen inTrypanosoma bruceiwe identified conserved proteins with an analogous asymmetric localisation in the related parasiteLeishmania mexicana. Using deletion mutants, we map which are necessary for normal cell swimming, flagellum beat parameters and axoneme ultrastructure, and using combinatorial endogenous fluorescent tagging and deletion, map co-dependencies for assembly into their normal asymmetric localisation. This revealed 15 proteins, 8 known and 7 novels, with a conserved proximal or distal axoneme-specific localisation. Most were outer dynein arm associated, and showed that there are at least two distinct classes of proximal-distal asymmetry – one dependent on the docking complex, and one independent. Many were necessary for normal frequency of the tip-to-base symmetric flagellar waveform, and our comprehensive mapping reveals unexpected contribution of proximal-specific axoneme components to frequency of distal waveform initiation.
Confounding of indirect genetic and epigenetic effects
Authors: Krätschmer Ilse , Robinson Matthew R.
Published: May 2024

An individual’s phenotype reflects a complex interplay of the direct effects of their DNA, epigenetic modifications of their DNA induced by their parents, and indirect effects of their parents’ DNA. Here, we present theory that shows there is a greater degree of potential confounding between direct, epigenetic imprinting, maternal and paternal genetic effects than has been previously considered, especially under assortative mating. We show how covariances among these effects contribute substantially to the population-level variance. Assortative mating alters the variance by inducing increased homozygosity and correlations within and across loci, which may lead to covariance of parental genetic effects, a measure of the similarity of the indirect genetic effects among parents on their children. We propose that this assortment for parental characteristics, where biological parents create similar environments for their children, can create shared parental effects across traits and the appearance of cross-trait assortative mating. Our results demonstrate that single-locus, marginal estimates commonly made in genome-wide association studies are impossible to interpret causally, even from within-family studies. Understanding the genetic basis of complex traits requires controlling for the covariances among loci across the genome (both cis- and trans-correlations) when estimating genetic effects, which could be achieved by fitting all variants and all forms of genetic effect (direct, maternal, paternal, parent-of-origin) jointly.
Pre-vaccination transcriptomic profiles of immune responders to the MUC1 peptide vaccine for colon cancer prevention
Authors: Cameron Cheryl M. , Raghu Vineet , Richardson Brian , Zagore Leah L. , Tamilselvan Banumathi , Golden Jackelyn , Cartwright Michael , Schoen Robert E. , Finn Olivera J. , Benos Panayiotis V. , Cameron Mark J.
Published: May 2024

Self-antigens abnormally expressed on tumors, such as MUC1, have been targeted by therapeutic cancer vaccines. We recently assessed in two clinical trials in a preventative setting whether immunity induced with a MUC1 peptide vaccine could reduce high colon cancer risk in individuals with a history of premalignant colon adenomas. In both trials, there were immune responders and non-responders to the vaccine. Here we used PBMC pre-vaccination and 2 weeks after the first vaccine of responders and non-responders selected from both trials to identify early biomarkers of immune response involved in long-term memory generation and prevention of adenoma recurrence. We performed flow cytometry, phosflow, and differential gene expression analyses on PBMCs collected from MUC1 vaccine responders and non-responders pre-vaccination and two weeks after the first of three vaccine doses. MUC1 vaccine responders had higher frequencies of CD4 cells pre-vaccination, increased expression of CD40L on CD8 and CD4 T-cells, and a greater increase in ICOS expression on CD8 T-cells. Differential gene expression analysis revealed that iCOSL, PI3K AKT MTOR, and B-cell signaling pathways are activated early in response to the MUC1 vaccine. We identified six specific transcripts involved in elevated antigen presentation, B-cell activation, and NF-κB1 activation that were directly linked to finding antibody response at week 12. Finally, a model using these transcripts was able to predict non-responders with accuracy. These findings suggest that individuals who can be predicted to respond to the MUC1 vaccine, and potentially other vaccines, have greater readiness in all immune compartments to present and respond to antigens. Predictive biomarkers of MUC1 vaccine response may lead to more effective vaccines tailored to individuals with high risk for cancer but with varying immune fitness.
MonoallelicTYROBPdeletion is a novel risk factor for Alzheimer’s disease
Authors: Martiskainen Henna , Willman Roosa-Maria , Heikkinen Sami , Müller Stephan A. , Sinisalo Rosa , Takalo Mari , Mäkinen Petra , Kuulasmaa Teemu , Pekkala Viivi , Galván del Rey Ana , Harju Päivi , Juopperi Sini-Pauliina , Jeskanen Heli , Kervinen Inka , Saastamoinen Kirsi ,   FinnGen, Niiranen Marja , Heikkinen Sami V. , Kurki Mitja I. , Marttila Jarkko , Mäkinen Petri I. , Ngandu Tiia , Lehtisalo Jenni , Bellenguez Céline , Lambert Jean-Charles , Haass Christian , Rinne Juha , Hakumäki Juhana , Rauramaa Tuomas , Krüger Johanna , Soininen Hilkka , Haapasalo Annakaisa , Lichtenthaler Stefan F. , Leinonen Ville , Solje Eino , Hiltunen Mikko
Published: May 2024

Biallelic loss-of-function variants inTYROBPandTREM2cause autosomal recessive presenile dementia with bone cysts known as Nasu-Hakola disease (NHD, alternatively polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy, PLOSL). Some otherTREM2variants contribute to the risk of Alzheimer’s disease (AD) and frontotemporal dementia, while deleteriousTYROBPvariants are globally extremely rare and their role in neurodegenerative diseases remains unclear. The population history of Finns has favored the enrichment of deleterious founder mutations, including a 5.2 kb deletion encompassing exons 1-4 ofTYROBPand causing NHD in homozygous carriers. We used here a proxy marker to identify monoallelicTYROBPdeletion carriers in the Finnish biobank study FinnGen combining genome and health registry data of 520,210 Finns. We show that monoallelicTYROBPdeletion associates with an increased risk and earlier onset age of AD and dementia when compared to noncarriers. In addition, we present the first reported case of a monoallelicTYROBPdeletion carrier with NHD-type bone cysts. Mechanistically, monoallelicTYROBPdeletion leads to decreased levels of DAP12 protein (encoded byTYROBP) in myeloid cells. Using transcriptomic and proteomic analyses of human monocyte-derived microglia-like cells, we show that upon lipopolysaccharide stimulation monoallelicTYROBPdeletion leads to the upregulation of the inflammatory response and downregulation of the unfolded protein response when compared to cells with two functional copies ofTYROBP. Collectively, our findings indicateTYROBPdeletion as a novel risk factor for AD and suggest specific pathways for therapeutic targeting.

One Sentence Summary

Nasu-Hakola disease causingTYROBPdeletion increases the risk of Alzheimer’s disease in elderly monoallelic carriers in the Finnish population.
Improvement in quality of life and cognitive function in Post Covid Syndrome after online occupational therapy: results from a randomized controlled pilot study
Authors: Schröder Dominik , Stölting Andrea , Müllenmeister Christina , Behrens Georg M.N. , Klawitter Sandra , Klawonn Frank , Cook Aisha , Wegner Nadja , Wetzke Martin , Schmachtenberg Tim , Dopfer-Jablonka Alexandra , Müller Frank , Happle Christine
Published: May 2024

Background

Post-COVID-Syndrome (PCS) poses enormous clinical challenges. Occupational therapy (OT) is recommended in PCS, but structural validation of this concept is pending.

Methods

In an unblinded randomized pilot study (clinical trial # DRKS0026007), feasibility and effects of online OT in PCS were tested. Probands received structured online OT over 12 weeks either via interactive online treatment sessions (interactive group) or prerecorded videos (video group). 50% of probands received no online OT (control group). At week 0, 12, and 24, we analyzed study experience, health-related quality of life, and impairment in performance, participation, and cognitive functions.

Results

N=158 probands (mean age 38 yrs., 86% female) were included into the analyses. 83.3% of probands in the interactive versus 48.1% of probands in the video group described their study experience as positive or very positive (p=0.001). After 12 weeks, all groups displayed significant improvement in concentration, memory, and performance of daily tasks. After 24 weeks, significant improvement in concentration and memory were observed in control- and video-probands, and social participation had improved after video-OT. However, only probands that had received interactive online OT showed improvement of all measured endpoints including concentration, memory, quality of life, and social participation.

Conclusion

We show that online OT is feasible and that interactive online OT is a promising treatment strategy for affected patients. We present exploratory data on its efficacy and describe variables that can be employed for further investigations in confirmatory trials.
Naa10 regulates hippocampal neurite outgrowthviaBtbd3 N-α-acetylation-mediated actin dynamics
Authors: Chou Chien-Te , Kang Ming-Lun , Lee Chen-Cheng , Hsu Pang-Hung , Juan Li-Jung
Published: May 2024

Protein N-α-acetylation is widespread in eukaryotes, yet its neuronal role remains unclear. Mutations in human N-α-acetyltransferase 10 (NAA10) lead to developmental defects affecting brain function, such as intellectual disability and autism. We found that hippocampal CA1-specificNaa10-knockout mice exhibit anxiety and reduced hippocampal dendritic complexity. Mechanistically, Naa10 promotes neurite outgrowth by acetylating BTB/POZ domain-containing protein 3 (Btbd3), crucial for the interaction of Btbd3 with filamentous actin (F-actin)-capping protein subunit beta (CapZb). Disrupting the Btbd3/CapZb interaction, either throughNaa10knockout or by expressing an N-α-acetylation-defective Btbd3 mutant, diminishes CapZb binding to F-actin and reduces neurite outgrowth. Moreover, cytochalasin D, a compound like CapZb in capping the barbed end of F-actin, rescues theNaa10knockout-induced neurite reduction in hippocampal primary neurons. These findings unveil the role of Naa10 in enhancing hippocampal neurite outgrowth through the Btbd3-CapZb-F-actin axis, shedding light on potential mechanisms underlying X-linked Ogden syndrome resulting from humanNAA10mutations.

eTOC

Chou et al. demonstrate that Naa10 promotes neurite outgrowth by N-acetylating Btbd3, facilitating the binding of the filamentous actin capping protein subunit beta (CapZb) to F-actin. Their study establishes a connection between protein N-α-acetylation and neuronal function, providing insight into the mechanism underlying brain disorders associated with human NAA10 mutations.

HIGHLIGHTS

Hippocampal CA1-specificNaa10KO leads to anxiety

Hippocampal CA1-specificNaa10KO reduces hippocampal dendritic complexity

Naa10 promotes neurite outgrowth by N-acetylating Btbd3

Naa10-mediated Btbd3 N-α-acetylation promotes CapZb binding to F-actin

Graphical Abstract
Single-Cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape
Authors: Song Lele , Li Qinglan , Xia Lingbo , Sahay Arushi , Qiu Qi , Li Yuanyuan , Li Haitao , Sasaki Kotaro , Susztak Katalin , Wu Hao , Wan Liling
Published: May 2024

Cell differentiation during organogenesis relies on precise epigenetic and transcriptional control. Disruptions to this regulation can result in developmental abnormalities and malignancies, yet the underlying mechanisms are not well understood. Wilms tumors, a type of embryonal tumor closely linked to disrupted organogenesis, harbor mutations in epigenetic regulators in 30-50% of cases. However, the role of these regulators in kidney development and pathogenesis remains unexplored. By integrating mouse modeling, histological characterizations, and single-cell transcriptomics and chromatin accessibility profiling, we show that a Wilms tumor-associated mutation in the chromatin reader protein ENL disrupts kidney development trajectory by rewiring the gene regulatory landscape. Specifically, the mutant ENL promotes the commitment of nephron progenitors while simultaneously restricting their differentiation by dysregulating key transcription factor regulons, particularly theHOXclusters. It also induces the emergence of abnormal progenitor cells that lose their chromatin identity associated with kidney specification. Furthermore, the mutant ENL might modulate stroma-nephron interactions via paracrine Wnt signaling. These multifaceted effects caused by the mutation result in severe developmental defects in the kidney and early postnatal mortality in mice. Notably, transient inhibition of the histone acetylation binding activity of mutant ENL with a small molecule displaces transcriptional condensates formed by mutant ENL from target genes, abolishes its gene activation function, and restores developmental defects in mice. This work provides new insights into how mutations in epigenetic regulators can alter the gene regulatory landscape to disrupt kidney developmental programs at single-cell resolutionin vivo. It also offers a proof-of-concept for the use of epigenetics-targeted agents to rectify developmental defects.
An empirical evaluation of simulated gastrointestinal digestion platforms for use in plant breeding, using common bean (Phaseolus vulgarisL.) as a model
Authors: Bolt Tayah M. , Riggs Margaret , Sun Weiyi , Tian Li , Gepts Paul , Palkovic Antonia , Parker Travis , Bornhorst Gail M. , Diepenbrock Christine
Published: May 2024

There remains a disconnect in plant breeding between increasing nutrient levels in crops at time of harvest and increasing bioaccessible levels of those nutrients during digestion. This study aims to develop and compare simulated digestion models for use in plant breeding and examine bioaccessible nutrient levels in common bean samples with differing seed coat coloration and patterning. The highest trait values (starch and protein hydrolysis, total phenolics, and antioxidant power) were observed from more dynamic digestion models, but even simple dynamic models showed higher trait values than a commonly used static digestion model. The use of these models provided insight on nutrient bioaccessibility; e.g., differences were observed during digestion between common bean genotypes for protein hydrolysis and between growing environments for both total phenolics and protein hydrolysis. Together, these results inform potential future pathways for applying simulated digestion models in plant breeding to improve bioaccessible nutrient levels in crops.
Linear ubiquitin chains remodel the proteome and influence the levels of hundreds of regulators inDrosophila
Authors: Nuga Oluwademilade , Richardson Kristin , Patel Nikhil , Wang Xusheng , Pagala Vishwajeeth , Stephan Anna , Peng Junmin , Demontis Fabio , Todi Sokol V.
Published: May 2024

Ubiquitin controls many cellular processes via its post-translational conjugation onto substrates. Its use is highly variable due to its ability to form poly-ubiquitin with various topologies. Among them, linear chains have emerged as important regulators of immune responses and protein degradation. Previous studies inDrosophila melanogasterfound that expression of linear poly-ubiquitin that cannot be dismantled into single moieties leads to their own ubiquitination and degradation or, alternatively, to their conjugation onto proteins. However, it remains largely unknown which proteins are sensitive to linear poly-ubiquitin. To address this question, here we expanded the toolkit to modulate linear chains and conducted ultra-deep coverage proteomics from flies that express non-cleavable, linear chains comprising 2, 4, or 6 moieties. We found that these chains regulate shared and distinct cellular processes inDrosophilaby impacting hundreds of proteins. Our results provide key insight into the proteome subsets and cellular pathways that are influenced by linear poly-ubiquitin with distinct lengths and suggest that the ubiquitin system is exceedingly pliable.
Systematic Development of Reprogrammed Modular Integrases Enables Precise Genomic Integration of Large DNA Sequences
Authors: Fauser Friedrich , Arangundy-Franklin Sebastian , Davis Jessica E , Liu Lifeng , Schmidt Nicola J , Rodriguez Luis , Scarlott Nicholas A , Mureli Rakshaa , Xia Danny F , Hinkley Sarah J , Kadam Bhakti N , Nguyen Nga , Lam Stephen , Bourgeois Bryan , Tait Emily , Qasim Mohammad , Vaidya Vishvesha , Chen Adeline , Nguyen Andrew , Li Patrick , Paschon David E , Davis Gregory D , Miller Jeffrey C
Published: May 2024

Despite recent progress in the ability to manipulate the genomes of eukaryotic cells1–3, there is still no effective and practical method to precisely integrate large synthetic DNA constructs into desired chromosomal sites using a programmable integrase. Serine integrases can perform the necessary molecular steps4, but only if their natural target site is first installed into the recipient genome by other methods. A more elegant approach would be to directly reprogram the serine integrase itself to target a desired site endogenous to the genome that is different from the natural recognition site of the integrase5. Here, we describe the development of a platform of Modular Integrases (the MINT platform), a versatile protein-guided genome editing method that can facilitate site-directed targeted integration of synthetic DNA into chromosomal sites. Through a combination of structural modeling, directed evolution, and screening in human cells we have reprogrammed the specificity of the serine integrase Bxb1. We then utilized these reprogrammed Bxb1 variants to enable precise integration of kilobase-sized constructs into multiple endogenous locations within the human genome with up to 35% efficiency and promising genome-wide specificity. We demonstrate the therapeutic potential of the MINT platform by retargeting Bxb1 to the human TRAC and AAVS1 loci where wild-type Bxb1 has no detectable activity.