bluuebunny/crossref_metadata_2025 huggingface dataset:
COMPUTATIONAL IDENTIFICATION VALIDATION AND STRUCTURAL CHARACTERIZATION OF SOME POTENTIAL CANDIDATE GENES FOR DIABETES MELLITUS
Authors: Tanty Dhananjay Kumar , Sahu Prachi Rani , Behera Swagatika , Mohapatra Ranjit , Behera Pabitra Mohan , Sahu Susanta Kumar
Published: August 2022

Diabetes mellitus seems to be a complex metabolic disorder due to its association with several complications like cardiovascular, ocular, neurologic, skeletal, hepatic and renal abnormalities etc. Current estimations by WHO suggest that most of the low and middle-income countries of the world are worst affected by this disorder with a prediction that the prevalence may double between 2020 and 2030. Thus both doctors and scientists across the globe are involved in research to disclose the complex genetics of this disorder associated with several environmental and demographic factors. In the last 10 years, several predictions have been made in the lane of omics approaches and computational biology which makes the process quite generous. In the current work, we present a computational analysis of potential candidate genes for diabetes mellitus and their differential expressions in targeted human tissue systems. About 220 reported genes for diabetes mellitus were selected for the study and their protein-protein interaction network (5090 nodes) was extracted using medium-confidence interactions of the HIPPIE database. From the network, the top 10% (509) genes were categorised as hub genes after calculation of about 11 centralities, their consensus ranking and rank correlations. The same set of 220 genes was used for gene ontology enrichment analysis featuring about 1483 genes. About 89 candidate genes were predicted for diabetes mellitus and their differential expressions were studied in adipose, pancreas, skeletal, hepatic and renal tissue systems using the information from NCBI GEOdatabase. Then the differentially expressed gene sets for each tissue system were further validated by fetching them in the potential clusters of the PPI network designed earlier with their functional enrichment analysis using information from the STRINGS database. About 77 genes were prioritized with help of our scoring system and their structural characterization was done with protein centric annotations from UniProtKB database information and molecular model building. We hope our findings are helpful in understanding the expression of diabetes-related genes in different human tissue systems which may lead to the design of newer therapeutic strategies.
Orthogonal Shared Basis Factorization: Cross-species gene expression analysis using a common expression subspace
Authors: Thomas Amal
Published: August 2022

One of the main challenges in analyzing gene expression profiles across species is the dependence on determining corresponding genes between species. Homology-based approaches fail to account for the contribution of non-homologous genes to the phenotype, genes’ functional divergence, and rewiring of pathways. Homology-independent methods based on joint matrix factorization provide a potential solution, but biological interpretations with existing approaches are difficult. We developed a novel joint matrix factorization method that we call the orthogonal shared basis factorization (OSBF) to compare functionally similar phenotypes across species. OSBF utilizes a similar correlation structure within individual datasets to estimate interpretable matrix factors. This homology-independent approach places cellular phenotypes in a common coordinate system that can summarize gene expression patterns shared by different organisms and quantifies the role of all genes in the phenotype independent of their homology relationships and annotation. OSBF is available on GitHub.
Disruption of lysosomal proteolysis in astrocytes facilitates midbrain proteostasis failure in an early-onset PD model
Authors: Parfitt Gustavo Morrone , Coccia Elena , Goldman Camille , Whitney Kristen , Reyes Ricardo , Sarrafha Lily , Nam Ki Hong , Sohail Soha , Jones Drew , Crary John F , Ordureau Alban , Blanchard Joel , Ahfeldt Tim D
Published: August 2022

Accumulation of advanced glycation end products (AGEs) on biopolymers accompany cellular aging and drives poorly understood disease processes. Here, we studied how AGEs contribute to development of early on-set Parkinson’s Disease (PD) caused by loss-of-function of DJ1, a protein deglycase. In induced pluripotent stem cell (iPSC)-derived midbrain organoid models deficient for DJ1 activity, we find that lysosomal proteolysis is impaired, causing AGEs to accumulate, α-synuclein (α-syn) phosphorylation to increase, and proteins to aggregate. These processes are at least partly driven by astrocytes, as DJ1 loss reduces their capacity to provide metabolic support and triggers acquisition of a pro-inflammatory phenotype. Consistently, in co-cultures, we find that DJ1-expressing astrocytes are able to reverse the proteolysis deficits of DJ1 knockout midbrain neurons. In conclusion, astrocytes’ capacity to clear toxic damaged proteins is critical to preserve neuronal function and their dysfunction contributes to the neurodegeneration observed in PD.
Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma
Authors: Ruiz-Moreno Cristian , Salas Sergio Marco , Samuelsson Erik , Brandner Sebastian , Kranendonk Mariette E.G. , Nilsson Mats , Stunnenberg Hendrik G.
Published: August 2022

Glioblastoma, isocitrate dehydrogenase (IDH)-wildtype (hereafter, GB), is an aggressive brain malignancy associated with a dismal prognosis and poor quality of life. Single-cell RNA sequencing has helped to grasp the complexity of the cell states and dynamic changes in GB. Large-scale data integration can help to uncover unexplored tumor pathobiology. Here, we resolved the composition of the tumor milieu and created a cellular map of GB (‘GBmap’), a curated resource that harmonizes 26 datasets gathering 240 patients and spanning over 1.1 million cells. We showcase the applications of our resource for reference mapping, transfer learning, and biological discoveries. Our results uncover the sources of pro-angiogenic signaling and the multifaceted role of mesenchymal-like cancer cells. Reconstructing the tumor architecture using spatially resolved transcriptomics unveiled a high level of well-structured neoplastic niches. The GBmap represents a framework that allows the streamlined integration and interpretation of new data and provides a platform for exploratory analysis, hypothesis generation and testing.
Long non-coding RNA RGMB-AS1 as a novel modulator of Bone Morphogenetic Protein Receptor 2 signaling in pulmonary arterial hypertension
Authors: Ali Md Khadem , Liu Yu , Zhao Lan , Wu Joseph C. , de Jesus Perez Vinicio , Rhodes Christopher J. , Cao Aiqin , Wilkins Martin R. , Nicolls Mark R. , Spiekerkoetter Edda F.
Published: August 2022

This study shows that the long non-coding RNA RGMB-AS1 is upregulated in the blood and pulmonary vascular cells of PAH patient and that it regulates BMPR2 signaling. Inhibiting RGMB-AS1 increases BMPR2 signaling and improves pulmonary vascular cell function.
Lipid droplets are intracellular mechanical stressors that promote hepatocyte dedifferentiation
Authors: Loneker Abigail E. , Alisafaei Farid , Kant Aayush , Janmey Paul A. , Shenoy Vivek B. , Wells Rebecca G.
Published: August 2022

Matrix stiffening and external mechanical stress have been linked to disease and cancer development in multiple tissues, including the liver, where cirrhosis (which increases stiffness markedly) is the major risk factor for hepatocellular carcinoma. Patients with non-alcoholic fatty liver disease and lipid-droplet-filled hepatocytes, however, can develop cancer in non-cirrhotic, relatively soft tissue. Here, we show that lipid droplets are intracellular mechanical stressors with similar effects to tissue stiffening, including nuclear deformation, chromatin condensation, and hepatocyte dedifferentiation. Mathematical modelling of lipid droplets as inclusions that have only mechanical interactions with other cellular components generated results consistent with our experiments. These data show that lipid droplets are intracellular sources of mechanical stress and suggest that nuclear membrane tension integrates cell responses to combined internal and external stresses.

Significance Statement

Deformation of the nucleus as a result of extracellular sources of stress, including increased substrate stiffness, constricted migration, and compression, has been well documented to lead to increased nuclear rupture, changes in gene expression, and accumulation of DNA damage. Lipid droplet accumulation in hepatocytes provides a unique scenario to investigate potential intracellular mechanical stresses and sources of nuclear deformation. Our results show that lipid droplets are significant mechanical elements in the cell, deforming the nucleus in a way that promotes hepatocyte dedifferentiation and resisting cytoskeletal contraction and alignment.
Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery
Authors: Ranathunga Dineli T. S. , Torabifard Hedieh
Published: August 2022

BRCA1 (BReast Cancer-Associated protein 1), a human tumor suppressor, plays a key role in genome stability and DNA repair. Heterodimerization of BRCA1 with BARD1 is important for its stability, maximal Ub ligase (E3) activity and cooperative activation of UbcH5c (E2). Recent studies demonstrate the importance of ubiquitination of the nucleosomal H2A C-terminal tail by BRCA1/BARD1-UbcH5c (E3-E2) in which its mutations inhibit ubiquitination, predispose cells to chromosomal instability and greatly increase the likelihood of breast and ovarian cancer development. Due to the lack of molecular-level insight on the flexible and disordered H2A C-tail, its ubiquitination mechanism by BRCA1/BARD1-UbcH5c and its function and relationship to cancer susceptibility remain elusive. Here, we use molecular dynamics simulations to provide molecular-level insights into the dynamics of the less-studied H2A C-tail and BRCA1/BARD1-UbcH5c on the nucleosome surface. Our results precisely identify the key interactions and residues that trigger conformational transitions of BRCA1/BARD1-UbcH5c, and characterize the important role of histone electrostatics in their dynamics. We show that the dynamics of the H2A C-tail, combined with the highly mobile UbcH5c, define the ubiquitination capacity. Furthermore, our data demonstrate a mechanistic basis for the probability of ubiquitination of C-tail lysines in the ordered and disordered regions. Altogether, the findings of this study will provide unrevealed insights into the mechanism of H2A C-tail ubiquitination and help us understand the communication between E2-E3 enzymes and nucleosome to regulate ubiquitination machinery, paving the way for the development of effective treatments for cancer and chronic pain.

Abstract Figure
Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds
Authors: Chakraborty Abhisek , Bisht Manohar S. , Saxena Rituja , Mahajan Shruti , Pulikkan Joby , Sharma Vineet K.
Published: August 2022

Bos indicus is a domestic cattle species with many indigenous breeds found in India and is important for dairy, draught work, and other household activities. Distinct phenotypic differences are observed among the breeds of this species; however, their whole genome sequences were not available. Therefore, in this study, we performed the whole genome sequencing using Illumina short-read technology to construct draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur, of which Vechur is known as the smallest cow of the world. We also report the first de novo genome assemblies of these native B. indicus breeds. Further, we constructed the 18S rRNA marker gene sequences of these B. indicus breeds, which were not yet known. Genomic analysis helped to identify the distinct bovine phenotypic characteristics-related and other biological process-related genes in this species compared to B. taurus, and to gain comparative genomic insights between the dwarf and non-dwarf breeds of this species.
Cell-type-specific whole-genome landscape of ΔFOSB binding in nucleus accumbens after chronic cocaine exposure
Authors: Yeh Szu-Ying , Estill Molly , Lardner Casey K. , Browne Caleb J. , Minier-Toribio Angelica , Futamura Rita , Beach Katherine , McManus Catherine A. , Xu Song-jun , Zhang Shuo , Heller Elizabeth A. , Shen Li , Nestler Eric J.
Published: August 2022

The ability of neurons to respond to external stimuli involves adaptations of gene expression. The transcription factor, ΔFOSB, is important for the development of drug addiction, however, its gene targets have not been identified. Here we use CUT&RUN to map the genome-wide enrichment of ΔFOSB binding in the two major neuronal cell types of the nucleus accumbens, a key brain reward region, after cocaine exposure. The binding landscape shows that the majority of ΔFOSB peaks occur outside of promoter regions, including intergenic regions, and are surrounded by epigenetic marks indicative of active enhancers. BRG1, the core subunit of the SWI/SNF chromatin remodeling complex, overlaps with ΔFOSB peaks, consistent with earlier studies of ΔFOSB’s interacting proteins. In addition, in silico analyses predict that ΔFOSB cooperatively regulates gene expression with homeobox and T-box transcription factors. These novel findings uncover key elements of ΔFOSB’s molecular mechanisms in transcriptional regulation.
Vector acquisition and co-inoculation of two plant viruses influences transmission, infection, and replication in new hosts
Authors: McLaughlin Autumn A. , Hanley-Bowdoin Linda , Kennedy George G. , Jacobson Alana L.
Published: August 2022

This study investigated the role of vector acquisition and transmission on the propagation of single and co-infections of tomato yellow leaf curl virus (TYLCV,) and tomato mottle virus (ToMoV) (Family: Geminiviridae, Genus: Begomovirus) by the whitefly vector Bemisia tabaci MEAM1 (Gennadius) in tomato. The aim of this research was to determine if how viruses are co-acquired and co-transmitted changes the probability of acquisition, transmission and new host infections. Whiteflies acquired virus by feeding on singly infected plants, co-infected plants, or by sequential feeding on singly infected plants. Viral titers were also quantified by qPCR in vector cohorts, in artificial diet, and plants after exposure to viruliferous vectors. Differences in transmission, infection status of plants, and titers of TYLCV and ToMoV were observed among treatments. All vector cohorts acquired both viruses, but co-acquisition/co-inoculation generally reduced transmission of both viruses as single and mixed infections. Co-inoculation of viruses by the vector also altered virus accumulation in plants regardless of whether one or both viruses were propagated in new hosts. These findings highlight the complex nature of vector-virus-plant interactions that influence the spread and replication of viruses as single and co-infections.
A pharmacoproteomic landscape of organotypic intervention responses in Gram-negative sepsis
Authors: Mohanty Tirthankar , Karlsson Christofer A. Q. , Chao Yashuan , Malmström Erik , Bratanis Eleni , Grentzmann Andrietta , Mørch Martina , Nizet Victor , Malmström Lars , Linder Adam , Shannon Oonagh , Malmström Johan
Published: August 2022

Sepsis is the major cause of mortality across intensive care units globally, yet details of accompanying pathological molecular events remains unclear. This knowledge gap has resulted in ineffective development of sepsis-specific biomarkers and therapies, and suboptimal treatment regimens to prevent or reverse organ damage. Here, we used pharmacoproteomics to score treatment effects in a murineEscherichia colisepsis model based on changes in the organ, cell, and plasma proteome landscapes. A combination of pathophysiological read-outs and time-resolved proteome maps of organs and blood enabled us to define time-dependent and organotypic proteotypes of dysfunction and damage upon administration of several combinations of the broad-spectrum beta-lactam antibiotic meropenem (Mem) and/or the immunomodulatory glucocorticoid methylprednisolone (Gcc). Three distinct response patterns were identified, defined as intervention-specific reversions, non-reversions, and specific intervention-induced effects, which depended on the underlying proteotype and varied significantly across organs. In the later stages of the disease, Gcc enhanced some positive treatment effects of Mem with superior reduction of the inflammatory response in the kidneys and partial restoration of sepsis-induced metabolic dysfunction. Unexpectedly, Mem introduced sepsis-independent perturbations in the mitochondrial proteome that were to some degree counteracted by Gcc. In summary, this study provides a pharmacoproteomic resource describing the time-resolved septic organ failure landscape across organs and blood, coupled to a novel scoring strategy that captures unintended secondary drug effects as an important criterion to consider when assessing therapeutic efficacy. Such information is critical for quantitative, objective, and organotypic assessment of benefits and unintended effects of candidate treatments in relationship to dosing, timing, and potential synergistic combinations in murine sepsis models.
Spatial transcriptomics reveals ovarian cancer subclones with distinct tumour microenvironments
Authors: Denisenko Elena , de Kock Leanne , Tan Adeline , Beasley Aaron B. , Beilin Maria , Jones Matthew E. , Hou Rui , Muirí Dáithí Ó , Bilic Sanela , Mohan G. Raj K. A. , Salfinger Stuart , Fox Simon , Hmon Khaing , Yeow Yen , Gray Elin S. , Cohen Paul A. , Yu Yu , Forrest Alistair R. R.
Published: August 2022

High-grade serous ovarian carcinoma (HGSOC) is characterised by recurrence, chemotherapy resistance and overall poor prognosis. Genetic heterogeneity of tumour cells and the microenvironment of the tumour have been hypothesised as key determinants of treatment resistance and relapse. Here, using a combination of spatial and single cell transcriptomics (10x Visium and Chromium platforms), we examine tumour genetic heterogeneity and infiltrating populations of HGSOC samples from eight patients with variable response to neoadjuvant chemotherapy. By inferring gross copy number alterations (CNAs), we identified distinct tumour subclones co-existing within individual tumour sections. These tumour subclones have unique CNA profiles and spatial locations within each tumour section, which were further validated by ultra-low-pass whole genome sequencing. Differential expression analysis between subclones within the same section identified both tumour cell intrinsic expression differences and markers indicative of different infiltrating cell populations. The gene sets differentially expressed between subclones were significantly enriched for genes encoding plasma membrane and secreted proteins, indicative of subclone-specific microenvironments. Furthermore, we identified tumour derived ligands with variable expression levels between subclones that correlated or anticorrelated with various non-malignant cell infiltration patterns. We highlight several of these that are potentially direct tumour-stroma/immune cell relationships as the non-malignant cell type expresses a cognate receptor for the tumour derived ligand. These include predictions of CXCL10-CXCR3 mediated recruitment of T and B cells to associate with the subclones of one patient and CD47-SIRPA mediated exclusion of macrophages from association with subclones of another. Finally, we show that published HGSOC molecular subtype signatures associated with prognosis are heterogeneously expressed across tumour sections and that areas containing different tumour subclones with different infiltration patterns can match different subtypes. Our study highlights the high degree of intratumoural subclonal and infiltrative heterogeneity in HGSOC which will be critical to better understand resistance and relapse.
Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility
Authors: Li Shuxiang , Wei Tiejun , Panchenko Anna R.
Published: August 2022

Nucleosomes containing the histone variant H2A.Z are important for gene transcription initiation and termination, chromosome segregation and DNA double-strand break repair, among other functions. However, the underlying mechanism of how H2A.Z influences nucleosome stability, dynamics and DNA accessibility remains elusive as experimental and computational evidence are inconclusive. Our modeling efforts of nucleosome stability and dynamics, along with comparisons with experimental data show that the incorporation of H2A.Z results in a substantial decrease of the energy barrier for DNA unwrapping. This leads to spontaneous DNA unwrapping of about forty base pairs in total, enhanced DNA accessibility, nucleosome gapping and histone plasticity, which otherwise is not observed for canonical nucleosomes. We demonstrate that both N- and C-terminal tails of H2A.Z play major roles in these events, whereas H3.3 variant exerts a negligible impact in modulating the DNA end unwrapping. In summary, our results indicate that H2A.Z deposition makes nucleosomes more mobile and DNA more accessible to transcriptional machinery and other chromatin components.
High throughput expression-based phenotyping and RNAi screening reveals novel regulators of planarian stem cells
Authors: Schad Erik G. , Petersen Christian P.
Published: August 2022

The complexity of cell types and states revealed by single-cell RNAseq atlases presents a challenge for the systematic analysis of fate determinants using traditional screening methodologies. Differentiation in the planarian Schmidtea mediterranea exemplifies this problem, as these animals continuously produce over 100 differentiated cell types for homeostasis and regeneration using neoblast adult pluripotent stem cells. The signaling factors enabling neoblast self-renewal and selective differentiation of these many fates are still incompletely understood. We developed a method using high-throughput expression profiling by qPCR and whole-animal RNAseq to simultaneously assess numerous cell fate markers as the phenotypic readout in large-scale RNAi screens. Applying this method, we performed an RNAi screen of 400 kinases, receptors, and other regulatory molecules to reveal specific functions for 30 previously unknown factors in neoblast biology. 17 genes were required for neoblast maintenance, including factors likely involved in cell-cycle regulation, nutrient sensing, and chromatin modification. Multidimensional expression information additionally revealed several specific regulators of other neoblast activities, including a mink1 kinase regulating global neoblast differentiation, the energy responsive kinase adenylate kinase-2 regulating intestine specification within the neoblast population, an RNA acetyl transferase nat10 regulating epidermal differentiation, and a pak1 kinase restricting neoblast localization to prevent tissue outgrowths. These results identify several new regulators of neoblast activities and demonstrate the applicability of expression-based screening for systematic analysis of stem cell phenotypes in whole animals.
Characterization of the structure and self-assembly of two distinct class IB hydrophobins
Authors: Kenward Calem , Vergunst Kathleen L. , Langelaan David N.
Published: August 2022

Hydrophobins are small proteins secreted by fungi that accumulate at interfaces, modify surface hydrophobicity, and self-assemble into large amyloid-like structures. These unusual properties make hydrophobins an attractive target for commercial applications as emulsifiers and surface modifying agents. Hydrophobins have diverse sequences and tertiary structures, complicating attempts to characterize how they function. Here we describe the atomic resolution structure of the unusual hydrophobin SLH4 and compare its function to another hydrophobin, SC16. Despite containing only one charged residue, SLH4 has a similar structure to SC16 yet has strikingly different rodlet morphology and propensity to self-assemble. Secondary structure analysis of both SC16 and SLH4 before and after assembly suggest that residues in the first intercysteine loop undergo conformational changes. This work outlines a representative structure for class IB hydrophobins and illustrates how hydrophobin surface properties govern self-assembly, which provides context to rationally select hydrophobins for applications as surface modifiers.

Keypoints

-The atomic-resolution structure of the hydrophobin SLH4 was determined using nuclear magnetic resonance spectroscopy

-The structure of SLH4 outlines a representative structure for class IB hydrophobins

-The assembly characteristics of SLH4 and SC16 are strikingly different, outlining how surface properties of hydrophobins influence their function.
A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference
Authors: Puritz Jonathan B. , Guo Ximing , Hare Matt , He Yan , Hillier LaDeana , Jin Shubo , Liu Ming , Lotterhos Katie , Minx Pat , Modak Tejashree , Proestou Dina , Rice Edward S. , Tomlinson Chad , Warren Wes , Witkop Erin , Zhao Honggang , Gomez-Chiarri Marta
Published: August 2022

Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster,Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed apost hocmethod to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig-masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.
Super-resolution imaging reveals dynamic reticular cytoophidia
Authors: Fang Yifan , Li Yi-Lan , Li Xiao-Ming , Liu Ji-Long
Published: August 2022

CTP synthase (CTPS) can form filamentous structures termed cytoophidia in cells from all three domains of life. In order to study the mesoscale structure of cytoophidia, we perform fluorescence recovery after photobleaching (FRAP) and stimulated emission depletion (STED) microscopy in human cells. By using EGFP dimeric tag, as a tool to explore the physical properties of cytoophidia, we find that cytoophidia are dynamic and reticular. The reticular structure of CTPS cytoophidia may provide space for other components such as IMPDH. In addition, we observe CTPS granules with tentacles.
Glial Reactivity and Cognitive Decline Follow Chronic Heterochromatin Loss in Neurons
Authors: Newman Andrew G , Sharif Jafar , Bessa Paraskevi , Zaqout Sami , Brown Jeremy , Richter Daniel , Dannenberg Rike , Nakayama Manabu , Mueller Susanne , Schaub Theres , Manickaraj Shairam , Böhm-Sturm Philipp , Ohara Osamu , Koseki Haruhiko , Singh Prim B , Tarabykin Victor
Published: August 2022

In aging cells and animal models of premature aging, heterochromatin loss coincides with transcriptional disruption including the activation of normally silenced endogenous retroviruses (ERVs). Here we show that loss of heterochromatin maintenance and de-repression of ERVs results in a chronic inflammatory environment characterized by neurodegeneration and cognitive decline. We discovered differential contributions of HP1 proteins to ERV silencing where HP1γ is necessary and sufficient for H4K20me3 deposition and HP1β deficiency causes aberrant DNA methylation. Combined loss of HP1β and HP1γ resulted in loss of DNA methylation at ERVK elements. Progressive ERV de-repression in HP1β/γ DKO mice was followed by stimulation of the integrated stress response, an increase of Complement 3+ reactive astrocytes and phagocytic microglia. This chronic inflammatory state coincided with age-dependent reductions in dendrite complexity and cognition. Our results demonstrate the importance of preventing loss of epigenetic maintenance, as this will be the only way postmitotic neuronal genomes can be protected and/or renewed.
Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: the SH2 domain of SH2B1
Authors: Fowler Nicholas J. , Albalwi Marym F. , Lee Subin , Hounslow Andrea M. , Williamson Mike P.
Published: August 2022

Protein structures calculated using NMR data are less accurate and less well defined than they could be. Here we use the program ANSURR to show that this deficiency is at least in part due to a lack of hydrogen bond restraints. We then describe a protocol to introduce hydrogen bond restraints into the structure calculation of the SH2 domain from SH2B1 in a systematic and transparent way, and show that the structures generated are more accurate and better defined as a result. We also show that ANSURR can be used as a guide to know when the structure calculation is good enough to stop.
Effect of beneficial sweeps and background selection on genetic diversity in changing environments
Authors: Kaushik Sachin
Published: August 2022

Neutral theory predicts that the genetic diversity within a population is proportional to the census population size. In contrast, observed genetic diversity for various species is much lower than theoretical prediction (Lewontin’s paradox). The selective sweeps and background selection, reduce the genetic variation at the linked neutral sites and have been studied considering the environment to be selectively constant. However, in a natural population, the selective environment varies with time. Here, we investigate the impact of selective sweeps and background selection on neutral genetic diversity when the selection coefficient changes periodically over time. The reduction in genetic variation due to selective sweeps is known to depend on the conditional fixation time. Here, we find that the effect of changing environment on conditional mean fixation time is most substantial for the randomly mating population than the inbreeding population with arbitrary inbreeding coefficient. We also study the effect of background selection on neutral sites when the selection co-efficient of linked deleterious mutation change periodically in time. In the slowly changing environment, we find that neutral heterozygosity is significantly different, and the site frequency spectrum has a different shape than that in the static environment.
Spontaneously blinking fluorophores for accelerated MINFLUX nanoscopy
Authors: Remmel Michael , Scheiderer Lukas , Butkevich Alexey N. , Bossi Mariano L. , Hell Stefan W.
Published: August 2022

Spontaneously blinking fluorophores, a class of molecules switching rapidly between a dark and a brightly emitting state, have emerged as a popular core to build fluorescent markers for super-resolution microscopy. With typical on-times in the order of tens of milliseconds, they are most suitable for STORM and related nanoscopy methods. Recent MINFLUX nanoscopy, however, can localize molecules even within a millisecond and achieve an up to ten times higher localization precision. Here, we present a series of spontaneous blinkers with short on-times (1-3 ms) matching MINFLUX recording time-scales. Our design builds upon a silicon rhodamine fluorescent core with a modified thiophene- or a benzothiophene-fused spirolactam fragment, which shifts the spirocyclization equilibrium toward the dark closed form at physiological conditions, imparting cell permeability. Concurrently, we obtain a highly photostable, short-lived open form with bright red emission. Characterizing the blinking behavior of single fluorophores bound to three different protein tags (antibodies, nanobodies, and HaloTag self-labeling enzyme) allowed us to select the best candidate for MINFLUX microscopy. The short on-times speed up MINFLUX localization by up to 30-fold.
In vivo visualization of nitrate dynamics using a genetically encoded biosensor
Authors: Chen Yen-Ning , Cartwright Heather , Ho Cheng-Hsun
Published: August 2022

Nitrate (NO3-) uptake and distribution are critical to plant life. Although the upstream regulation of nitrate uptake and downstream responses to nitrate in a variety of cells have been well-studied, it is still not possible to directly visualize the spatial and temporal distribution of nitrate with high resolution at the cellular level. Here, we report a nuclear-localized, genetically encoded biosensor, nlsNitraMeter3.0, for the quantitative visualization of nitrate distribution in Arabidopsis thaliana. The biosensor tracked the spatiotemporal distribution of nitrate along the primary root axis and disruptions by genetic mutation of transport (low nitrate uptake) and assimilation (high nitrate accumulation). The developed biosensor effectively monitors nitrate concentrations at cellular level in real time and spatiotemporal changes during the plant life cycle.

One-Sentence Summary

A genetically encoded biosensor for in vivo visualization of spatiotemporal nitrate levels at a cellular resolution.
The evo-MOTiF pipeline and database for studying protein motif evolution in a structural context
Authors: de Boissier Paul , Zweig Nathanael , Habermann Bianca H.
Published: August 2022

Short linear motifs (SLiMs) in proteins are short functionally independent sequence stretches with a defined function and required for proteins to interact with their environment. Their functional importance makes it interesting to analyse SLiM features further, such as their structural or evolutionary properties, to understand better how SLiMs evolve to shape protein functions.

We developed an automated pipeline to analyse features of SLiMs, called evo-MOTiF. This pipeline takes as input a single protein sequence and its associated SLiM(s) and returns a set of scores associated with SLiM features, including their disorder, as well as their overall, positional and amino acid property conservation. To store and easily mine data from the evo-MOTiF pipeline, we developed the evo-MOTiF database, which currently holds ∼9500 motifs, combining data from ELM, PhosphoSitePlus, as well as from cross-linking mass-spectrometry (XL-MS) experiments. The evo-MOTiF database distinguishes itself further by allowing effortless filtering for SLiMs with specific properties, such as disorder, or conservation in evolution and by providing evolutionary, as well as structural information for SLiMs. Preliminary analysis of SLiM features reveals weak negative correlation between disorder and overall, positional, as well as amino acid property conservation, which is in support of previous observations on smaller datasets.

The evo-MOTiF pipeline and database are freely available athttps://gitlab.com/habermann_lab/slimsandhttp://etnadb.ibdm.univ-mrs.fr/index.php, respectively.
OHP2 is not required for psbA translation in Chlamydomonas
Authors: Wang Fei , Dischinger Korbinian , Westrich Lisa Désirée , Meindl Irene , Egidi Felix , Trösch Raphael , Sommer Frederik , Johnson Xenie , Schroda Michael , Nickelsen Joerg , Willmund Felix , Vallon Olivier , Bohne Alexandra-Viola
Published: August 2022

In land plants and cyanobacteria, co-translational association of chlorophyll (Chl) to the nascent D1 polypeptide, a reaction center protein of photosystem II (PSII), requires a Chl binding complex consisting of a short-chain dehydrogenase (HCF244/Ycf39) and One-Helix Proteins of the LHC superfamily (OHP1 and OHP2 in chloroplasts). Here, we show that an ohp2 mutant of the green alga Chlamydomonas reinhardtii fails to accumulate core PSII subunits, in particular D1. Extragenic suppressors arise at high frequency, suggesting the existence of another route for Chl association to PSII. The ohp2 mutant can be complemented by the Arabidopsis ortholog. In contrast to land plants, where psbA translation is prevented in the absence of OHP2, ribosome profiling experiments show that the Chlamydomonas mutant translates the psbA transcript over its full length. Pulse labelling suggests that D1 is degraded during or immediately after translation. The translation of other PSII subunits is affected by assembly-controlled translational regulation (the CES process). Proteomics show that HCF244, a translation factor which associates with and is stabilized by OHP2 in land plants, still partly accumulates in the Chlamydomonas ohp2 mutant, explaining the persistence of psbA translation. Several Chl biosynthesis enzymes overaccumulate in the mutant membranes. Partial inactivation of the D1-degrading FtsH protease restores a low level of PSII activity in an ohp2 background, but not photoautotrophy. Taken together, our data suggest that OHP2 is not required for psbAD1 translation in Chlamydomonas, but necessary for its stabilization.
A Small Subset of Cytosolic dsRNAs Must Be Edited by ADAR1 to Evade MDA5-Mediated Autoimmunity
Authors: Sun Tao , Li Qin , Geisinger Jonathan M. , Hu Shi-Bin , Fan Boming , Su Shichen , Tsui Waitang , Guo Hongchao , Ma Jinbiao , Li Jin Billy
Published: August 2022

The innate immune system detects viral infection via pattern recognition receptors and induces defense reactions such as production of type I interferon1. One such receptor, MDA5, is activated upon the recognition of double-stranded RNAs (dsRNAs) that are often produced during viral replication2. Endogenous dsRNAs evade MDA5 activation through RNA editing by ADAR1, thus preventing autoimmunity3-5. Among the large number of endogenous dsRNAs, the key substrates whose editing is critical to evade MDA5 activation (termed as immunogenic dsRNAs) remain elusive. Here we reveal the identity of human immunogenic dsRNAs, a surprisingly small fraction of all cellular dsRNAs, to fill the gap in the ADAR1-dsRNA-MDA5 axis. We found that, in contrast to previous findings6,7, the immunogenic dsRNAs were highly enriched in mRNAs and depleted of introns, an expected indication of bona fide substrates of cytosolic MDA5. The immunogenic dsRNAs, in contrast to non-immunogenic dsRNAs, tended to have shorter loop between the stems, which may facilitate dsRNA formation. They also tended to be enriched at the GWAS signals of common inflammatory diseases, implying that they are truly immunogenic. We validated the MDA5-dependent immunogenicity of the dsRNAs, which was dampened following ADAR1-mediated RNA editing. We anticipate that a focused analysis of immunogenic dsRNAs will greatly facilitate the understanding and treatment of cancer and inflammatory diseases in which the important roles of dsRNA editing and sensing continue to be revealed8-13.
Reduced methionine synthase (Mtr) expression creates a functional vitamin B12 deficiency that leads to uracil accumulation in mouse mitochondrial DNA
Authors: Heyden Katarina E. , Fiddler Joanna L. , Xiu Yuwen , Malysheva Olga V. , Handzlik Michal K. , Phinney Whitney N. , Stiles Linsey , Stabler Sally S. , Metallo Christian M. , Caudill Marie A. , Field Martha S.
Published: August 2022

Adequate thymidylate (dTMP or the “T” base in DNA) levels are essential for stability of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). Folate and vitamin B12 (B12) are essential cofactors in folate-mediated one carbon metabolism (FOCM), a metabolic network which supports synthesis of nucleotides (including dTMP) and methionine. Perturbations in FOCM impair dTMP synthesis, causing misincorporation of uracil (or a “U” base) into DNA. During B12 deficiency, cellular folate accumulates as 5-methyltetrahdryfolate (5-methyl-THF), limiting nucleotide synthesis. The purpose of this study was to determine how B12 deficiency and dietary folate interact to affect mtDNA integrity and mitochondrial function in mouse liver. Mice expressing reduced methionine synthase (Mtr) levels were used to create a functional B12 deficiency. Folate accumulation, uracil levels, mtDNA content, and oxidative phosphorylation capacity were measured in male Mtr+/+ and Mtr+/- mice weaned onto either a folate-sufficient control diet (2 mg/kg folic acid, C) or a folate-deficient diet (FD, lacking folic acid) for 7 weeks. Mtr heterozygosity led to increased liver 5-methyl-THF levels. Mtr+/- mice consuming the C diet also exhibited a 40-fold increase in uracil in liver mtDNA. However, the combination of Mtr heterozygosity and exposure to the FD diet partially alleviated the level of uracil accumulation in mtDNA. Furthermore, Mtr+/- mice exhibited a 25% decrease in liver mtDNA content and a 20% decrease in maximal oxygen consumption rates. Impairments in mitochondrial FOCM are known to lead to increased uracil in mtDNA. This study demonstrates that impaired cytosolic dTMP synthesis also leads to increased uracil in mtDNA.
Structure of angiogenin dimer bound to double-stranded RNA
Authors: Sievers Katharina , Ficner Ralf
Published: August 2022

Angiogenin is an unusual member of the RNase A family and is of great interest in multiple pathological contexts. Although it has been assigned various regulatory roles, its core catalytic function is that of an RNA endonuclease. However, its catalytic efficiency is comparatively low and this has been linked to a unique C-terminal helix which partially blocks its RNA-binding site. Assuming that binding to its RNA substrate could trigger a conformational rearrangement, much speculation has arisen on the topic of the interaction of angiogenin with RNA. To date, no structural data on angiogenin–RNA interactions have been available. Here, the structure of angiogenin bound to a double-stranded RNA duplex is reported. The RNA does not reach the active site of angiogenin and no structural arrangement of the C-terminal domain is observed. However, angiogenin forms a previously unobserved crystallographic dimer that makes several backbone interactions with the major and minor grooves of the RNA double helix.
Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states
Authors: Chen Aochiu , Mindrebo Jeffrey T. , Davis Tony D. , Kim Woojoo E. , Katsuyama Yohei , Jiang Ziran , Ohnishi Yasuo , Noel Joseph P. , Burkart Michael D.
Published: August 2022

Ketosynthases (KSs) catalyse essential carbon–carbon bond-forming reactions in fatty-acid biosynthesis using a two-step, ping-pong reaction mechanism. In Escherichia coli, there are two homodimeric elongating KSs, FabB and FabF, which possess overlapping substrate selectivity. However, FabB is essential for the biosynthesis of the unsaturated fatty acids (UFAs) required for cell survival in the absence of exogenous UFAs. Additionally, FabB has reduced activity towards substrates longer than 12 C atoms, whereas FabF efficiently catalyses the elongation of saturated C14 and unsaturated C16:1 acyl-acyl carrier protein (ACP) complexes. In this study, two cross-linked crystal structures of FabB in complex with ACPs functionalized with long-chain fatty-acid cross-linking probes that approximate catalytic steps were solved. Both homodimeric structures possess asymmetric substrate-binding pockets suggestive of cooperative relationships between the two FabB monomers when engaged with C14 and C16 acyl chains. In addition, these structures capture an unusual rotamer of the active-site gating residue, Phe392, which is potentially representative of the catalytic state prior to substrate release. These structures demonstrate the utility of mechanism-based cross-linking methods to capture and elucidate conformational transitions accompanying KS-mediated catalysis at near-atomic resolution.
A C2 continuous trajectory planning method for 6-DOF rotational robot manipulators
Authors: Min Kang , Ni Fenglei , Zhang Guojun , Shu Xin , Liu Hong
Published: August 2022

Purpose

The purpose of this paper is to propose a smooth double-spline interpolation method for six-degree-of-freedom rotational robot manipulators, achieving the global C2 continuity of the robot trajectory.

Design/methodology/approach

This paper presents a smooth double-spline interpolation method, achieving the global C2 continuity of the robot trajectory. The tool center positions and quaternion orientations are first fitted by a cubic B-spline curve and a quartic-polynomial-based quaternion spline curve, respectively. Then, a parameter synchronization model is proposed to realize the synchronous and smooth movement of the robot along the double spline curves. Finally, an extra u-s function is used to record the relationship between the B-spline parameter and its arc length parameter, which may reduce the feed rate fluctuation in interpolation. The seven segments jerk-limited feed rate profile is used to generate motion commands for algorithm validation.

Findings

The simulation and experimental results demonstrate that the proposed method is effective and can generate the global C2-continuity robot trajectory.

Originality/value

The main contributions of this paper are as follows: guarantee the C2 continuity of the position path and quaternion orientation path simultaneously; provide a parameter synchronization model to realize the synchronous and smooth movement of the robot along the double spline curves; and add an extra u-s function to realize arc length parameterization of the B-spline path, which may reduce the feed rate fluctuation in interpolation.
Human vs robot baristas during the COVID-19 pandemic: effects of masks and vaccines on perceived safety and visit intention
Authors: Choi Miju , Choi Youngjoon , Kim Seongseop (Sam) , Badu-Baiden Frank
Published: August 2022

Purpose

This study aims to compare the effect of barista type (human vs robot) on perceived safety and examine the role of two moderators (mask-wearing and coronavirus vaccination) on the effects of barista type on perceived safety and visit intention.

Design/methodology/approach

The research design consists of three studies. Three experiments were sequentially designed and conducted to address research questions.

Findings

Study 1 found that perceived safety mediates the effect of barista type on customers’ visit intention. Study 2 revealed that the mask-wearing of human and robot baristas differently influences perceived safety. Study 3 showed that customers, especially where robot baristas are used, perceive the effect of mask-wearing differently depending on their coronavirus vaccination status.

Research limitations/implications

Given that the levels of restrictions vary worldwide, together with the extent of countries’ vaccination rollouts, caution is required when generalising the research findings.

Practical implications

The findings have practical implications for the hospitality industry, where the roles of face masks and coronavirus vaccines in shaping consumer psychology and behaviour have been underexplored.

Originality/value

Coronavirus vaccination is considered one of the most important driving forces for the recovery of hospitality businesses. As a heuristic-systematic model postulated, this study identified that vaccination status (fully vaccinated vs not vaccinated) changes the level of involvement when customers assess the level of risk in service environments. By pinpointing the function of service robots in safeguarding customers from the potential spread of the disease, this study broadens the scope of human–robot interaction research in hospitality.