bluuebunny/crossref_metadata_2025 huggingface dataset:
Potassium dependent structural changes in the selectivity filter of HERG potassium channels
Authors: Lau Carus H.Y. , Flood Emelie , Hunter Mark J. , Williams-Noonan Billy J , Corbett Karen M. , Ng Chai-Ann , Bouwer James C. , Stewart Alastair G. , Perozo Eduardo , Allen Toby W. , Vandenberg Jamie I.
Published: December 2023

The fine tuning of biological electrical signaling is mediated by variations in the rates of opening and closing of gates that control ion flux through different ion channels. Human ether-a-go-go related gene (HERG) potassium channels have uniquely rapid inactivation kinetics which are critical to the role they play in regulating cardiac electrical activity. Here, we have exploited the K+sensitivity of HERG inactivation to determine structures of both a conductive and non-conductive selectivity filter structure of HERG. We propose that inactivation is the result of a high propensity for flipping of the selectivity filter valine carbonyl oxygens. Molecular dynamics simulations point to a low energy barrier, and hence rapid kinetics, for flipping of the valine 625 carbonyl oxygens facilitated by a previously unrecognized interaction between S620 and Y616 that stabilizes the transition state between conducting and non-conducting structures. Our model represents a new mechanism by which ion channels fine tune their activity that explains the uniquely rapid inactivation kinetics of HERG.

Highlights

Structures of a conductive and non-conductive HERG selectivity filter have been determined.

Reduced potassium causes flipping of selectivity filter valine carbonyl oxygens.

The sidechain of S620 on the pore helix coordinates distinct sets of interactions between conductive, non-conductive, and transition states.
Acute Neuropixels recordings in the marmoset monkey
Authors: Dotson Nicholas M. , Davis Zachary W. , Jendritza Patrick , Reynolds John H.
Published: December 2023

High-density linear probes, like Neuropixels, provide an unprecedented opportunity to understand how neural populations within specific laminar compartments contribute to behavior. Marmoset monkeys, unlike macaque monkeys, have a lissencephalic (smooth) cortex that enables recording perpendicular to the cortical surface, thus making them an ideal animal model for studying laminar computations. Here we present a method for acute Neuropixels recordings in the common marmoset (Callithrix jacchus). The approach replaces the native dura with an artificial silicon-based dura that grants visual access to the cortical surface, which is helpful in avoiding blood vessels, ensures perpendicular penetrations, and could be used in conjunction with optical imaging or optogenetic techniques. The chamber housing the artificial dura is simple to maintain with minimal risk of infection and could be combined with semi-chronic microdrives and wireless recording hardware. This technique enables repeated acute penetrations over a period of several months. With occasional removal of tissue growth on the pial surface, recordings can be performed for a year or more. The approach is fully compatible with Neuropixels probes, enabling the recording of hundreds of single neurons distributed throughout the cortical column.
Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs
Authors: O’Leary Kevin , Zheng Deyou
Published: December 2023

Background

By resolving cellular heterogeneity in a biological sample, single cell RNA sequencing (scRNA-seq) can detect gene expression and its dynamics in different cell types. Its application to time-series samples can thus identify temporal genetic programs active in different cell types, for example, immune cells’ responses to viral infection. However, current scRNA-seq analysis need improvement. Two issues are related to data generation. One is that the number of genes detected in each cell is relatively low especially when currently popular dropseq-based technology is used for analyzing thousands of cells or more. The other is the lack of sufficient replicates (often 1-2) due to high cost of library preparation and sequencing. The third issue lies in the data analysis –-usage of individual cells as independent sampling data points leads to inflated statistics.

Methods

To address these issues, we explore a new data analysis framework, specifically whether “metacells” that are carefully constructed to maintain cellular heterogeneity within individual cell types (or clusters) can be used as “replicates” for statistical methods requiring multiple replicates. Toward this, we applied SEACells to a time-series scRNA-seq dataset from peripheral blood mononuclear cells (PBMCs) after SARS-Cov-2 infection to construct metacells, which were then used in maSigPro for quadratic regression to find significantly differentially expressed genes (DEGs) over time, followed by clustering analysis of the expression velocity trends.

Results

We found that metacells generated using the SEACells algorithm retained greater between-cell variance and produced more biologically meaningful results compared to metacells generated from random cells. Quadratic regression revealed significant DEGs through time that have been previously annotated in the SARS-CoV2 infection response pathway. It also identified significant genes that have not been annotated in this pathway, which were compared to baseline expression and showed unique expression patterns through time.

Conclusions

The results demonstrated that this strategy could overcome the limitation of 1-2 replicates, as it correctly identified the known ISG15 interferon response program in almost all PBMC cell types. Its application further led to the uncovering of additional and more cell type-specific gene expression programs that potentially modulate different levels of host response after infection.
Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9
Authors: Eggers Amy R. , Chen Kai , Soczek Katarzyna M. , Tuck Owen T. , Doherty Erin E. , Thornton Brittney W. , Xu Bryant , Trinidad Marena I. , Doudna Jennifer A.
Published: December 2023

Thermostable CRISPR-Cas9 enzymes could improve genome editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold higher genome editing levels. Cryo-EM structures of the wildtype and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome editing activity.
Effective seed sterilization methods require optimization across maize genotypes
Authors: Parnell J. Jacob , Pal Gaurav , Awan Ayesha , Vintila Simina , Houdinet Gabriella , Hawkes Christine V. , Balint-Kurti Peter J. , Wagner Maggie R. , Kleiner Manuel
Published: December 2023

Studies of plant-microbe interactions using synthetic microbial communities (SynComs) often require the removal of seed-associated microbes by seed sterilization prior to inoculation to provide gnotobiotic growth conditions. A diversity of seed sterilization protocols have been developed in the past and have been used on different plant species with various amounts of validation. From these studies it has become clear that each plant species requires its own optimized sterilization protocol. It has, however, so far not been tested if the same protocol works equally well for different varieties and seed sources of one plant species. We evaluated six seed sterilization protocols on two different varieties (Sugar Bun & B73) of maize. All unsterilized maize seeds showed fungal growth upon germination on filter paper, highlighting the need for a sterilization protocol. A short sterilization protocol with hypochlorite and ethanol was sufficient to prevent fungal growth on Sugar Bun germinants, however a longer protocol with heat treatment and germination in fungicide was needed to obtain clean B73 germinants. This difference may have arisen from the effect of either genotype or seed source. We then tested the protocol that performed best for B73 on three additional maize genotypes from four sources. Seed germination rates and fungal contamination levels varied widely by genotype and geographic source of seeds. Our study shows that consideration of both variety and seed source is important when optimizing sterilization protocols and highlights the importance of including seed source information in plant-microbe interaction studies that use sterilized seeds.
An optimized method for gene knockdown in differentiating human and mouse adipocyte cultures
Authors: Chua Ruiming , Ghosh Sujoy
Published: December 2023

Adipocyte cultures are a mainstay of metabolic disease research, yet loss-of-function studies in differentiating adipocytes is complicated by the refractoriness of lipid-containing adipocytes to standard siRNA transfections. Alternative methods, such as electroporation or adenovirus/lentivirus-based delivery systems are complex, expensive and often accompanied with unacceptable levels of cell death. To address this problem, we have tested two commercially available siRNA delivery systems in this study using a multi-parameter optimization approach. Our results identified a uniform siRNA transfection protocol that can be applied to human and mouse adipocyte cultures throughout the time course of differentiation, beginning with pre-differentiated cells and continuing up to lipid-accumulated differentiated adipocytes. Our findings allow for efficient transfection of human and mouse adipocyte cultures using standard and readily available methodologies, and should help significantly expand the scope of gene manipulation studies in these cell types.
On-device edge-learning for cardiac abnormality detection using a bio-inspired and spiking shallow network
Authors: Huang Zhaojing , Leung Wing Hang , Yu Leping , Herbozo Contreras Luis Fernando , Zhang Ziyao , Truong Nhan Duy , Nikpour Armin , Kavehei Omid
Published: December 2023

This work presents an on-device edge-learning for cardiac abnormality detection by developing a hybrid and spiking form of 2-Dimensional (time-frequency) Convolutional Long-Short-Term Memory (ConvLSTM2D) with Closed-form Continuous-time (CfC) neural network (sCCfC), which is a bio-inspired shallow network. The model achieves an F1 score and AUROC of 0.82 and 0.91 in cardiac abnormalities detection. These results are comparable to the non-spiking ConvLSTM2D-CfC (ConvCfC) model1. Notably, the sCCfC model demonstrates a significantly higher energy efficiency with an estimated power consumption of 4.68µJ/Inf (per inference) on an emulated Loihi’s neuromorphic chip architecture, in contrast to ConvCfC model’s consumption of 450µJ/Inf on a conventional processor. Additionally, as a proof-of-concept, we deployed the sCCfC model on the conventional and relatively resource-constrained Radxa Zero, which is equipped with Amlogic S905Y2 processor foron-device training, which resulted in performance improvements. After initial training of 2 epochs on a conventional GPU, the F1 score and AUROC improved from 0.46 and 0.65 to 0.56 and 0.73 respectively with 5 additional epochs of on-device training. Furthermore, when presented with a new dataset, the sCCfC model showcases strong out-of-sample generalization capabilities that can constitute a pseudo-perspective test, achieving an F1 score and AUROC of 0.71 and 0.86. The spiking sCCfC also outperforms the non-spiking ConvCfC model in robustness regarding effectively handling missing ECG channels during inference. The model’s efficacy extends to single-lead electrocardiogram (ECG) analysis, demonstrating reasonable accuracy in this context, while the focus of our work has been on the computational and memory complexities of the model.
Chromosome-level genome assembly for Sichuan taimen (hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage
Authors: Zhang Xinmiao , Xiong Dongmei , Jian Shenglong , Jiang Yu , Wang Lixin
Published: December 2023

Salmonid fishes are globally renowned and valuable, with most members of the Salmonidae family living in seawater and exhibiting migratory behavior. In contrast, huchonid fishes (Hucho spp.and Brachymystax spp.), an ancient evolutionary branch within Salmoninae, are entirely landlocked. The Sichuan taimen (Hucho bleekeri Kimura) is a critically endangered fish that has attracted widespread concern and is one of eleven national first-level protected fishes in China. However, genome resources for all Hucho spp., including H. bleekeri, are scarce, and the genomic characteristics of this ancient evolutionary lineage remain unclear, hindering conservation biology efforts. Here, we present the first chromosome-level genome for the Sichuan taimen, with a final genome size of approximately 3.45 Gb across 44 chromosomes. The Sichuan taimen genome contains 44.15% tandem repetitive sequences, exceeding those of all sequenced salmonid fishes. We also identified 44 Ss4R homeologous block pairs in the assembled genome. Genome synteny analysis suggested a ~5 fold tandem repeat expansion in the Sichuan taimen compared to the Salmonidae ancestor Northern pike. Phylogenetic analysis estimated the divergence time between huchonid and other Salmoninae fishes at approximately 33.29 million years ago (Mya). The divergence time between Siberia taimen and Sichuan taimen was estimated at around 2.29 Mya, with their effective population size declining from around 1 Mya. The genomic resource provided in this article will promote the protection of the Sichuan taimen and evolutionary genetics studies of salmonids.
A versatile and upgraded version of the LundTax classification algorithm applied to independent cohorts
Authors: Aramendía Cotillas Elena , Bernardo Carina , Veerla Srinivas , Liedberg Fredrik , Sjodahl Gottfrid , Eriksson Pontus
Published: December 2023

Stratification of cancer into biologically and molecularly similar subgroups is a cornerstone of precision medicine and transcriptomic profiling has revealed that urothelial carcinoma (UC) is a heterogeneous disease with several distinct molecular subtypes. The Lund Taxonomy classification system for urothelial carcinoma aims to be applicable across the whole disease spectrum including both non-muscle invasive and invasive bladder cancer. For a classification system to be useful it is of critical importance that it can be applied robustly and reproducibly to new samples. Many transcriptomic methods used for subtype classification are affected by the choice of expression platform, data preprocessing, cohort composition, and tumor purity. The application of a subtype classification system across studies therefore comes with a degree of uncertainty regarding whether the predictions in a new cohort accurately recapitulate the originally intended stratification. Currently, only limited data has been published evaluating the transferability and applicability of existing stratification systems and their respective classification-algorithms to external datasets. In the present investigation we develop a single sample classifier based on in-house microarray and RNA-sequencing data intended to be broadly applicable across datasets, studies, and tumor stages. We evaluate the performance of the proposed method and the Lund Taxonomical classification across 10 published bladder cancer cohorts (n=2560 cases) by examining the expression of characteristic subtype associated gene signatures, and whether complementary data such as mutations, clinical outcomes, response, or variant histologies are captured by our classification. Effects of varying sample purity on the classification results were also evaluated by generating low-purity versions of samples in silico. We show that the classifier is robustly applicable across different gene expression profiling platforms and preprocessing methods, and less sensitive to variations in sample purity.

The classifier is available as the ‘LundTaxonomy2023Classifier’ R package onGitHub.
A site-specific analysis of the ADP-Ribosylome unveils Homogeneous DNA Damage-Induced Serine ADP-Ribosylation across wild-type and BRCA-mutant Breast Cancer cell lines
Authors: Anagho Holda A. , Mullari Meeli , Prósz Aurél G. , Buch-Larsen Sara C. , Locard-Paulet Marie , Szallasi Zoltan , Nielsen Michael L.
Published: December 2023

ADP-ribosylation (ADPr) signaling plays a crucial role in the DNA damage response. Inhibitors against the main enzyme catalyzing ADPr after DNA damage – PARP1 – are used as targeted therapies against breast cancers with BRCA1/2 mutations. However, development of resistance to PARP inhibitors (PARPi) is a major obstacle in treating patients. To better understand the role of ADPr in PARPi sensitivity, we used Liquid Chromatography-Mass Spectrometry (LC-MS) for systems level analysis of the ADP-ribosylome in six breast cancer cell lines exhibiting different PARPi sensitivities. We identified 1,632 sites on 777 proteins across all cell lines, primarily on serine residues, with site-specific overlap of targeted residues across DNA damage-related proteins across all cell lines, demonstrating high conservation of serine ADPr signaling networks upon DNA damage. We furthermore observed site-specific differences in ADPr intensities in PARPi-sensitive BRCA mutants, and unique ADPr sites in PARPi-resistant BRCA mutant cells, which we notably show to have low PARG levels and longer ADPr chains on PARP1.
Parallel Molecular Data Storage by Printing Epigenetic Bits on DNA
Authors: Zhang Cheng , Wu Ranfeng , Sun Fajia , Lin Yisheng , Zhang Yizheng , Liang Yuan , Chen Yiming , Teng Jiongjiong , Song Zichen , Liu Na , Ouyang Qi , Qian Long , Yan Hao
Published: December 2023

DNA storage has shown potential to transcend current silicon-based data storage technologies in storage density, lifetime and energy consumption. However, writing large-scale data directly into DNA sequences byde novosynthesis remains uneconomical in time and cost. Inspired by the natural genomic modifications, in this work, we report an alternative, parallel strategy that enables the writing of arbitrary data on DNA using premade nucleic acids. With epigenetic modifications as information bits, our system employed DNA self-assembly guided enzymatic methylation to perform movable-type printing on universal DNA templates. By programming with a finite set of 700 DNA movable types and 5 templates, we achieved the synthesis-free writing of ∼270000 bits on an automated platform with 350 bits written per reaction. The data encoded in complex epigenetic patterns were retrieved high-throughput by nanopore sequencing, and algorithms were developed to finely resolve 240 modification patterns per sequencing reaction. Our framework presents a new modality of DNA-based data storage that is parallel, programmable, stable and scalable. Such a modality opens up avenues towards practical data storage and dual-mode data functions in biomolecular systems.
Claudin-4 polymerizes after the incorporation of just two extracellular claudin-3 residues
Authors: van der Veen Rozemarijn E. , Piontek Jörg , Bieck Marie , Saiti Arbesa , Gonschior Hannes , Lehmann Martin
Published: December 2023

Tight junctions play a pivotal role in the functional integrity of the human body by forming barriers crucial for tissue compartmentalization and protecting the body from external threats. Essential components of tight junctions are the transmembrane claudin proteins, which can polymerize into tight junction strands and meshworks. This study delves into the structural determinants of claudin polymerization, utilizing the close homology yet strong difference in polymerization capacity between claudin-3 and claudin-4. Through a combination of sequence alignment and structural modeling, critical residues in the second extracellular segment are pinpointed. Molecular dynamics simulations provide insights into the interactions of and the conformational changes induced by the identified extracellular segment 2 residues, shedding light on the intricacies of claudin polymerization. Live-STED imaging demonstrates that introduction of these residues from claudin-3 into claudin-4 significantly enhances polymerization in non-epithelial cells. In tight junction-deficient epithelial cells, mutated claudin-4 not only influences tight junction morphology but also partially restores barrier function. Understanding the structural basis of claudin polymerization is of paramount importance, as it offers insights into the dynamic nature of tight junctions. This knowledge could be applied to targeted therapeutic interventions, offering insight to repair or prevent barrier defects associated with pathological conditions, or introduce temporary barrier openings during drug delivery.
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation
Authors: Varshney Arushi , Manickam Nandini , Orchard Peter , Tovar Adelaide , Ventresca Christa , Zhang Zhenhao , Feng Fan , Mears Joseph , Erdos Michael R , Narisu Narisu , Nishino Kirsten , Rai Vivek , Stringham Heather M , Jackson Anne U , Tamsen Tricia , Gao Chao , Yang Mao , Koues Olivia I , Welch Joshua D , Burant Charles F , Williams L Keoki , Jenkinson Chris , DeFronzo Ralph A , Norton Luke , Saramies Jouko , Lakka Timo A , Laakso Markku , Tuomilehto Jaakko , Mohlke Karen L , Kitzman Jacob O , Koistinen Heikki A , Liu Jie , Boehnke Michael , Collins Francis S , Scott Laura J , Parker Stephen C J
Published: December 2023

Skeletal muscle, the largest human organ by weight, is relevant in several polygenic metabolic traits and diseases including type 2 diabetes (T2D). Identifying genetic mechanisms underlying these traits requires pinpointing cell types, regulatory elements, target genes, and causal variants. Here, we use genetic multiplexing to generate population-scale single nucleus (sn) chromatin accessibility (snATAC-seq) and transcriptome (snRNA-seq) maps across 287 frozen human skeletal muscle biopsies representing nearly half a million nuclei. We identify 13 cell types and integrate genetic variation to discover>7,000 expression quantitative trait loci (eQTL) and>100,000 chromatin accessibility QTLs (caQTL) across cell types. Learning patterns of e/caQTL sharing across cell types increased precision of effect estimates. We identify high-resolution cell-states and context-specific e/caQTL with significant genotype by context interaction. We identify nearly 2,000 eGenes colocalized with caQTL and construct causal directional maps for chromatin accessibility and gene expression. Almost 3,500 genome-wide association study (GWAS) signals across 38 relevant traits colocalize with sn-e/caQTL, most in a cell-specific manner. These signals typically colocalize with caQTL and not eQTL, highlighting the importance of population-scale chromatin profiling for GWAS functional studies. Finally, our GWAS-caQTL colocalization data reveal distinct cell-specific regulatory paradigms. Our results illuminate the genetic regulatory architecture of human skeletal muscle at high resolution epigenomic, transcriptomic, and cell-state scales and serve as a template for population-scale multi-omic mapping in complex tissues and traits.
An Integrated Optogenetic and Bioelectronic Platform for Regulating Cardiomyocyte Function
Authors: Bolonduro Olurotimi A. , Chen Zijing , Lai Yan-Ru , Cote Megan , Rao Akshita A. , Liu Haitao , Tzanakakis Emmanuel S. , Timko Brian P.
Published: December 2023

We report an integrated optogenetic and bioelectronic platform for stable and long-term modulation and monitoring of cardiomyocyte function in vitro. Optogenetic inputs were achieved through expression of a photoactivatable adenylyl cyclase (bPAC), that when activated by blue light caused a dose-dependent and time-limited increase in autonomous cardiomyocyte beat rate. Bioelectronic readouts were achieved through an integrated planar multi-electrode array (MEA) that provided real-time readouts of electrophysiological activity from 32 spatially-distinct locations. Irradiation at 27 μW/mm2resulted in a ca. 14% increase in beat rate within 20-25 minutes, which remained stable for at least 2 hours. The beating rate could be cycled through repeated “on” and “off” states, and its magnitude was a monotonic function of irradiation intensity. Our integrated platform opens new avenues in bioelectronic medicine, including closedloop feedback systems, with potential applications for cardiac regulation including arrhythmia diagnosis and intervention.

Teaser

A system that integrates optogenetic stimulation and bioelectronic recording capabilities allows for on-demand regulation of cardiac cell function.
Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation
Authors: Kefalopoulou Samy , Rullens Pim M. J. , de Luca Kim L. , de Vries Sandra S. , Korthout Tessy , van Oudenaarden Alexander , Zeller Peter , Kind Jop
Published: December 2023

The regulation of gene expression is governed at multiple levels of chromatin organization. However, how coordination is achieved remains relatively unexplored. Here we present Dam&ChIC, a method that enables time-resolved and multifactorial chromatin profiling at high resolution in single cells. Analysis of genome-lamina interactions in haploid cells reveals highly dynamic spatial repositioning of small domains during interphase and partial inheritance over mitosis. Dam&ChIC applied to study random X-inactivation uncovers that spreading of H3K27me3 on the inactive X chromosome (Xi) overlaps with remarkable genome-lamina detachment. We find that genome-lamina detachment precedes H3K27me3 accumulation on the Xi and occurs upon mitotic exit. Domains that retain genome-lamina interactions are marked by high pre-existing H3K9me3 levels. These findings imply an important role for genome-lamina interactions in regulating H3K27me3 accumulation on the Xi. We anticipate that Dam&ChIC will be instrumental in unraveling the interconnectivity and order of chromatin events underlying cell-state changes in single cells.
Impact of climate change and oligotrophication on quality and quantity of lake primary production: A case study in Lake Biwa
Authors: Kazama Takehiro , Hayakawa Kazuhide , Nagata Takamaru , Shimotori Koichi , Imai Akio
Published: December 2023

Global climate change and anthropogenic oligotrophication are expected to reshape the dynamics of primary production (PP) in aquatic ecosystems; however, few studies have explored their long-term effects. In theory, the PP of phytoplankton in Lake Biwa may decline over decades due to warming, heightened stratification, and anthropogenic oligotrophication. Furthermore, the PP of large phytoplankton, which are inedible to zooplankton, along with biomass-specific productivity (PBc), could decrease. In this study, data from 1976–2021 and active fluorometry measurements taken in 2020 and 2021 were evaluated. Quantitatively, the temporal dynamics of mean seasonal PP during 1971–2021 were assessed according to the carbon fixation rate to investigate relationships among environmental factors. Qualitatively, phytoplankton biomass, PP, and PBc were measured in two size fractions [edible (S) or inedible (L) for zooplankton] in 2020 and 2021, and the L:S balance for these three measures was compared between 1992 (low-temperature/high-nutrient conditions) and 2020–2021 (high-temperature/low-nutrient conditions) to assess seasonal dynamics. The results indicated that climate change and anthropogenic oligotrophication over the past 50 years have diminished Lake Biwa’s PP since the 1990s, impacting the phenology of PP dynamics. However, the L:S balance in PP and PBc has exhibited minimal change since 1992. These findings suggest that, although climate change and oligotrophication may reduce overall PP, they do not markedly alter the inedible/edible phytoplankton balance in terms of PP and PBc. Instead, as total PP declines, the production of small edible phytoplankton decreases proportionally, potentially affecting trophic transfer efficiency and material cycling in Lake Biwa.
Encompassing view of spatial and single-cell RNA-seq renews the role of the microvasculature in human atherosclerosis
Authors: Bleckwehl Tore , Maryam Sidrah , Babler Anne , Nyberg Michael , Bosteen Markus , Halder Maurice , Pyke Charles , Hvid Henning , Voetmann Louise Marie , Sluimer Judith C. , Das Vivek , Baumgart Simon , Kramann Rafael , Hayat Sikander
Published: December 2023

Atherosclerosis is a pervasive contributor to cardiovascular diseases including ischemic heart disease and stroke. Despite the advance and success of effective lipid lowering-therapies and hypertensive agents, the residual risk of an atherosclerotic event remains high and improving disease understanding and development of novel therapeutic strategies has proven to be challenging. This is largely due to the complexity of atherosclerosis with a spatial interplay of multiple cell types within the vascular wall. Here, we generated an integrative high-resolution map of human atherosclerotic plaques by combining single-cell RNA-seq from multiple studies and novel spatial transcriptomics data from 12 human specimens to gain insights into disease mechanisms. Comparative analyses revealed cell-type and atherosclerosis-specific expression changes and associated alterations in cell-cell communication. We highlight the possible recruitment of lymphocytes via different endothelial cells of the vasa vasorum, the migration of vascular smooth muscle cells towards the lumen to become fibromyocytes, and cell-cell communication in the plaque, indicating an intricate cellular interplay within the adventitia and the subendothelial space in human atherosclerosis.
Pneumococcal Extracellular Vesicles Mediate Horizontal Gene Transfer via the Transformation Machinery
Authors: Lass Sarah Werner , Camphire Shaw , Smith Bailey E. , Eutsey Rory A. , Prentice Jojo A. , Yerneni Saigopalakrishna S. , Arun Ashni , Bridges Andrew A. , Rosch Jason W. , Conway James F. , Campbell Phil , Hiller N. Luisa
Published: December 2023

Bacterial cells secrete extracellular vesicles (EVs), the function of which is a matter of intense investigation. Here, we show that the EVs secreted by the human pathogenStreptococcus pneumoniae(pneumococcus) are associated with bacterial DNA on their surface and can deliver this DNA to the transformation machinery of competent cells. These findings suggest that EVs contribute to gene transfer in Gram-positive bacteria, and in doing so, may promote the spread of drug resistance genes in the population.

Significance

This work extends our understanding of horizontal gene transfer and the roles of extracellular vesicles in pneumococcus. This bacterium serves as the model for transformation, a process by which bacteria can take up naked DNA from the environment. Here we show that extracellular vesicles secreted by the pneumococcus have DNA on their surface, and that this DNA can be imported by the transformation machinery facilitating gene transfer. Understanding EV-mediated gene transfer may provide new avenues to manage the spread of antibiotic drug resistance.
Impact of Cell Shape on Mitotic Spindle Positioning Forces
Authors: Xie Jing , Najafi Javad , Nommick Aude , Lederer Luc , Salle Jeremy , Dmitrieff Serge , Minc Nicolas
Published: December 2023

Cell geometry is a key parameter for the regulation of mitotic spindle positioning during early embryo development and tissue morphogenesis. To date, however, we still lack an understanding for how intracellular forces that position, orient or hold mitotic spindles depend on cell geometry. Here, we usedin vivomagnetic tweezers to directly measure the forces that maintain the mitotic spindle in the center of sea urchin cells that adopt different shapes during early embryo development. We found that spindles are held by viscoelastic forces that progressively increase in amplitude as cells become more elongated during early development. By coupling direct cell shape manipulations andin vivoforce measurements, we establish how spindle associated forces increase in dose dependence with cell shape anisotropy. Cytoplasm flow analysis and hydrodynamic simulations suggest that this geometry-dependent mechanical enhancement results from a stronger hydrodynamic coupling between the spindle and cell boundaries, which dampens cytoplasm flows and spindle mobility as cells become more elongated. These findings establish how cell shape affects spindle associated forces, and suggest a novel mechanism for shape-sensing and division positioning mediated by intracellular hydrodynamics with functional implications for early embryo morphogenesis.
Darkness inhibits autokinase activity of bacterial bathy phytochromes
Authors: Huber Christina , Strack Merle , Schultheiß Isabel , Pielage Julia , Mechler Xenia , Hornbogen Justin , Diller Rolf , Frankenberg-Dinkel Nicole
Published: December 2023

Bathy phytochromes are a subclass of bacterial biliprotein photoreceptors that carry a biliverdin IXα chromophore. In contrast to prototypical phytochromes that adopt a Pr ground state, the Pfr-form is the thermally stable ground state of bathy phytochromes. Although the photobiology of bacterial phytochromes has been extensively studied since their discovery in the late 1990s, our understanding of the signal transduction process to the connected transmitter domains, which are often histidine kinases, remains insufficient. Initiated by the analysis of the bathy phytochromePaBphP fromPseudomonas aeruginosa, we performed a systematic analysis of five different bathy phytochromes with the aim to derive a general statement on the correlation of photostate and autokinase output. While all proteins adopt different Pr/Pfr-fractions in response to red, blue, and far-red light, only darkness leads to a pure or highly-enriched Pfr-form, directly correlated with the lowest level of autokinase activity. Using this information, we developed a method to quantitatively correlate the autokinase activity of phytochrome samples with well-defined stationary Pr/Pfr-fractions. We demonstrate that the off-state of the phytochromes is the Pfr-form and that different Pr/Pfr-fractions enable the organisms to fine-tune their kinase output in response to a certain light environment. Furthermore, the output response is regulated by the rate of dark reversion, which differs significantly from 5 seconds to 50 minutes half-life. Overall, our study indicates that bathy phytochromes function as sensors of light and darkness, rather than red and far-red light, as originally postulated.
SRRM2 splicing factor modulates cell fate in early development
Authors: Carvalho Silvia , Zea-Redondo Luna , Tang Tsz Ching Chloe , Stachel-Braum Philipp , Miller Duncan , Caldas Paulo , Kukalev Alexander , Diecke Sebastian , Grosswendt Stefanie , Grosso Ana Rita , Pombo Ana
Published: December 2023

Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. Alternative splicing is modulated during development as an additional layer of regulation to reprogram gene expression patterns. TheSrrm2splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show thatSrrm2dosage is critical for maintaining embryonic stem cell pluripotency and cell identity.Srrm2heterozygosity promotes loss of stemness, characterized by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum- response transcription factor and differentiation-related genes. Depletion ofSrrm2by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 half-dosage are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles ofSrrm2in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis.

Summary statement

This article emphasizes the importance of splicing regulators in early mammalian development by uncovering roles of SRRM2 splicing factor dosage in pluripotency, providing novel insights for a better understanding of Srrm2-related diseases.
SARS-CoV-2 and other coronaviruses in rats, Berlin, Germany, 2023
Authors: Wernike Kerstin , Mehl Calvin , Aebischer Andrea , Heising Mario , Ulrich Rainer G. , Beer Martin
Published: December 2023

We tested 130 rats trapped in Berlin for coronaviruses. Antibodies against SARS-CoV-2 were detected in a single animal only, but not in further 66 rats from the same location, speaking against virus circulation in the rat population. All animals tested negative for SARS-CoV-2 by RT-PCR. However, rodent-associated alphacoronaviruses were found.
A genome wide CRISPR screen reveals that HOXA9 promotes Enzalutamide resistance in prostate cancer
Authors: Roes Michael V. , Dick Frederick A.
Published: December 2023

Androgen receptor inhibitors are commonly used for prostate cancer treatment, but acquired resistance is a significant problem. Co-deletion of RB and p53 is common in castration resistant prostate cancers, however they are difficult to target pharmacologically. To comprehensively identify gene loss events that contribute to enzalutamide response, we performed a genome-wide CRISPR knockout screen in LNCaP prostate cancer cells. This revealed novel genes implicated in resistance that are largely unstudied. Gene loss events that confer enzalutamide sensitivity are enriched for GSEA categories related to stem cell and epigenetic regulation. We investigated the myeloid lineage stem cell factor HOXA9 as a candidate gene whose loss promotes sensitivity to enzalutamide. Cancer genomic data reveals that HOXA9 overexpression correlates with poor prognosis and characteristics of advanced prostate cancer. In cell culture, HOXA9 depletion sensitizes cells to enzalutamide, whereas overexpression drives enzalutamide resistance. Combination of the HOXA9 inhibitor DB818 with enzalutamide demonstrates synergy. This demonstrates the utility of our CRISPR screen data in discovering new approaches for treating enzalutamide resistant prostate cancer.
Spatial, temporal and numerical regulation of polar flagella assembly inPseudomonas putida
Authors: Pulido-Sánchez Marta , Leal-Morales Antonio , López-Sánchez Aroa , Cava Felipe , Govantes Fernando
Published: December 2023

The Gram-negative bacteriumPseudomonas putidabears a tuft of flagella at a single cell pole. New flagella must be assembledde novoevery cell cycle to secure motility of both daughter cells. Here we show that the coordinated action of FimV, FlhF and FleN sets the location, timing and number of flagella assembled. The polar landmark proteins FimV and FlhF are independently targeted to the nascent new pole during or shortly after cell division, but FimV stabilizes FlhF association with the cell poles. FlhF determines the polar position of the flagella by targeting early flagellar components to the cell pole and preventing their nucleation at non-polar sites. FlhF also promotes efficient flagellar assembly and indirectly stimulates Class III flagellar promoter activation by promoting secretion of the anti-FliA anti-σ factor FlgM. The MinD-like ATPase FleN partitions between the cell poles and the cytoplasm. Cytoplasmic FleN regulates flagellar number by preventing excessive accumulation of FlhF at the cell poles that may otherwise lead to hyperflagellation, likely by antagonizing FleQ-dependent transcriptional activation. FimV is essential to FleN polar location. FimV and FleN temporally regulate the onset of flagellar assembly by preventing premature polar targeting of FlhF and the ensuing premature targeting of additional flagellar components. Our results shed new light on the mechanisms that ensure the timely assembly of the appropriate number of flagella at the correct polar location in polarly flagellated bacteria.

HIGHLIGHTS

FimV, FlhF and FleN determine the position, number and timing of flagellar assembly

FimV is essential to the normal intracellular distribution of FlhF and FleN

FlhF restricts flagellar location to the cell poles and promotes efficient assembly

Soluble, cytoplasmic FleN prevents polar FlhF accumulation and hyperflagellation

Pole-bound FimV and FleN prevent premature FlhF recruitment and flagellar assembly

GRAPHICAL ABSTRACT
A Fungal Spore Calendar for England: Analysis of 13 years of Daily Concentrations at Leicester, UK
Authors: Symon F. A. , Anees-Hill S. , Satchwell J. , Fairs A. , Edwards R. , Wardlaw A. J. , Cuthbertson L. , Hansell A. , Pashley C. H.
Published: December 2023

Background

Fungal respiratory allergy is believed to affect up to 30% of hayfever sufferers and up to 70% of severe asthmatics in the UK, however trends in fungal spore seasonality are not well described. Information about seasonal trends would help allergists determine sources of fungal sensitisation and aid disease management.

Method

Daily monitoring was carried out at Leicester from 2007 to 2020 using a Burkard volumetric spore trap. Fungal spore concentrations were analysed by microscopy, identifying 23 morphologically distinct taxa. Daily average concentrations were calculated as spores/m3of air sampled and a 90% method used to determine the spore seasons.

Results

Thirteen years of data were used to develop a fungal spore calendar for the nine most abundant spore types identified;Alternaria, Cladosporium, Didymella, Leptosphaeria, Sporobolomyces, TilletiopsisandUstilagoplus the wider groupings ofAspergillus/Penicilliumtype and coloured basidiospores. All have been implicated in fungal allergy.

We observed long seasons for,Cladosporium, SporobolomycesandTilletiopsis, beginning in late spring and ending in late autumn. In contrastUstilagoand the highly allergenicAlternariashowed relatively short seasons, spanning summer and early autumn. Temperature and precipitation were the main meteorological factors related to spore concentration with wind speed appearing to have little influence. Over the study period, there was a reducing trend for total spore concentrations, driven by a reduction in “wet weather” spores, in line with a reduction in precipitation. Conversely, the “dry weather” spores ofAlternariaandCladosporiumdemonstrated an increasing trend.

Conclusion

We present an aeroallergen calendar to provide readily accessible information to patients, healthcare professionals and pharmaceutical companies on exposure concentrations over the year in central England and potentially more widely across the UK. More research on allergenic thresholds would enhance the clinical usefulness of aeroallergen calendars.
Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
Authors: Lin Yingxin , Wu Tung-Yu , Chen Xi , Wan Sheng , Chao Brian , Xin Jingxue , Yang Jean Y.H. , Wong Wing H. , Wang Y.X. Rachel
Published: December 2023

Single-cell technologies offer unprecedented opportunities to dissect gene regulatory mechanisms in context-specific ways. Although there are computational methods for extracting gene regulatory relationships from scRNA-seq and scATAC-seq data, the data integration problem, essential for accurate cell type identification, has been mostly treated as a standalone challenge. Here we present scTIE, a unified method that integrates temporal multimodal data and infers regulatory relationships predictive of cellular state changes. scTIE uses an autoencoder to embed cells from all time points into a common space by using iterative optimal transport, followed by extracting interpretable information to predict cell trajectories. Using a variety of synthetic and real temporal multimodal data sets, we show scTIE achieves effective data integration while preserving more biological signals than existing methods, particularly in the presence of batch effects and noise. Furthermore, on the exemplar multiome data set we generated from differentiating mouse embryonic stem cells over time, we show scTIE captures regulatory elements highly predictive of cell transition probabilities, providing new potentials to understand the regulatory landscape driving developmental processes.
Orientational ordering and assembly of silica–nickel Janus particles in a magnetic field
Authors: Manna Gouranga , Zinn Thomas , Sharpnack Lewis , Narayanan Theyencheri
Published: December 2023

The orientation ordering and assembly behavior of silica–nickel Janus particles in a static external magnetic field were probed by ultra small-angle X-ray scattering (USAXS). Even in a weak applied field, the net magnetic moments of the individual particles aligned in the direction of the field, as indicated by the anisotropy in the recorded USAXS patterns. X-ray photon correlation spectroscopy (XPCS) measurements on these suspensions revealed that the corresponding particle dynamics are primarily Brownian diffusion [Zinn, Sharpnack & Narayanan (2023). Soft Matter, 19, 2311–2318]. At higher fields, the magnetic forces led to chain-like configurations of particles, as indicated by an additional feature in the USAXS pattern. A theoretical framework is provided for the quantitative interpretation of the observed anisotropic scattering diagrams and the corresponding degree of orientation. No anisotropy was detected when the magnetic field was applied along the beam direction, which is also replicated by the model. The method presented here could be useful for the interpretation of oriented scattering patterns from a wide variety of particulate systems. The combination of USAXS and XPCS is a powerful approach for investigating asymmetric colloidal particles in external fields.
A comparative study on the corrosion behavior of Q235 steel in saturated acidic red and yellow soils
Authors: Li Yingying , Liu Lanlan , Wang Jun , Xu Song , Su Hui , Xie Yi , Wu Tangqing
Published: December 2023

Purpose

The purpose of this paper is to study the corrosion behavior of Q235 steel in saturated acidic red and yellow soils.

Design/methodology/approach

The corrosion behavior of Q235 steel in saturated red and yellow soils was compared by weight-loss, SEM/EDS, 3D ultra-depth microscopy and electrochemical measurements.

Findings

Rp of the steel gradually increases and icorr gradually decreases in both the red and yellow soils with time. The Rp of the steel in the red soil is lower, but its icorr is higher than that in the yellow soil. The uniform corrosion rate, diameter and density of the corrosion pit on the steel surface in the red soil are greater than those in the yellow soil. Lower pH, higher contents of corrosive anions and high-valence Fe oxides in the red soil are responsible for its higher corrosion rates and local corrosion susceptibility.

Originality/value

This paper investigates the difference in corrosion behavior of carbon steel in saturated acidic red and yellow soils, which can help to understand the mechanism of soil corrosion.