bluuebunny/crossref_metadata_2025 huggingface dataset:
The mechanism of bacterial defense system DdmDE fromLactobacillus casei
Authors: Huang Pingping , Yan Purui , Guo Lijie , Fei Wenying , Li Zhaoxing , Liu Jingxian , Kong Jianping , Yao Yue , Lu Meiling , Xiao Yibei , Chen Meirong
Published: October 2024

Bacteria has developed a diverse array of defense mechanisms to protect against invasion by mobile genetic elements. Recent study identified a bacterial defense module DdmDE system which encodes a helicase-nuclease fusion protein DdmD and a putative prokaryotic Argonaute-like protein DdmE, imposing fitness advantages to the bacteria by eliminating invasive plasmids. However, the mechanistic basis of how DdmDE system detects and degrades plasmids is not fully understood. Here, by studying the DdmDE system fromLactobacillus casei(LcDdmDE), we found that LcDdmD is able to degrade ssDNA and nick plasmids in the presence of Mn2+, and it exhibits 5’-3’ DNA helicase activity in a ssDNA length-dependent mechanism. Meanwhile, LcDdmD serves as a sensor that utilizes DNA guide to recognize target DNA. We determined the cryo-EM structures of LcDdmD dimer bound with fork DNA, guide/target DNA-bound LcDdmE, and the complex of LcDdmDE-bubble DNA in intermediate state as well as active state. Together with functional analysis, we revealed the working mechanism of LcDdmDE system. In such a scenario, guided by ssDNA, LcDdmE recruits auto-inhibited LcDdmD dimer loading onto DNA target. Through substantial conformational changes, LcDdmD dimer dissociates into active monomer and unwind duplex for plasmid degradation. Our study provides structural insights into the mechanism of DdmDE, presenting pAgo-directed plasmid degradation by the allosterically regulated helicase-nuclease.
Regulatory Changes in the Fatty Acid ElongaseeloFUnderlie the Evolution of Sex-specific Pheromone Profiles inDrosophila prolongata
Authors: Luo Yige , Takau Ayumi , Li Jiaxun , Fan Tiezheng , Hopkins Ben R. , Le Yvonne , Ramirez Santiago R. , Matsuo Takashi , Kopp Artyom
Published: October 2024

Pheromones play a key role in regulating sexual behavior throughout the animal kingdom. InDrosophilaand other insects, many cuticular hydrocarbons (CHCs) are sexually dimorphic, and some are known to perform pheromonal functions. However, the genetic control of sex-specific CHC production is not understood outside of the model speciesD. melanogaster. A recent evolutionary change is found inD. prolongata, which, compared to its closest relatives, shows greatly increased sexual dimorphism in both CHCs and the chemosensory system responsible for their perception. A key transition involves a male-specific increase in the proportion of long-chain CHCs. PerfumingD. prolongatafemales with the male-biased CHCs reduces copulation success, suggesting that these compounds function as sex pheromones. The evolutionary change in CHC profiles correlates with a male-specific increase in the expression of multiple genes involved in CHC biosynthesis, including fatty acid elongases and reductases and other key enzymes. In particular,elongase F, which is responsible for producing female-specific pheromones inD. melanogaster, is strongly upregulated inD. prolongatamales compared both to females and to males of the sibling species. Induced mutations ineloFreduce the amount of long-chain CHCs, resulting in a partial feminization of pheromone profiles inD. prolongatamales while having minimal effect in females. Transgenic experiments show that sex-biased expression ofeloFis caused in part by a putative transposable element insertion in its regulatory region. These results reveal one of the genetic mechanisms responsible for a recent evolutionary change in sexual communication.
AxSpA joint tissue is characterised by HLA-DR+tissue resident memory (TRM) and killer cell immunoglobulin-like receptor (KIR)+CD8+T cell subsets
Authors: Liu Feng , Shi Hui , Chen Jiewei , Kendrick Ben , Du Dajiang , Bowness Paul , Tong Qiang , Chen Liye
Published: October 2024

Objective

Axial Spondyloarthritis (AxSpA) is a common inflammatory arthritis withHLA-B*27as the major genetic risk. Recent discoveries of AxSpA-specific T cell receptor (TCR) motifs and the self and bacterial peptides that they recognize support a pathogenic role of CD8+T cells. Despite of previous work on synovial fluid, the characteristics of CD8 cells in joint tissue are currently unknown.

Method

Synovial tissues from 5 AxSpA patients were used for single cell RNA sequencing (scRNA-seq). Paired TCR sequencing was carried out for 2. The abundance of KIR+CD8+T cells in the blood from 9 AxSpA patients and 10 healthy controls was measured using flow cytometry. The expression of naïve and memory T cell markers (CCR7, CD45RA and CD45RO) were compared between KIR+and KIR-CD8 cells.

Results

We observed conventional,TRAV1-2+mucosal-associated invariant T (MAIT) cell andMKI67+proliferating cell populations in synovium. Following sub-clustering of conventional CD8+T cells,HLA-DR+tissue resident memory (TRM), circulating,KIR+andFCGR3A+(encoding CD16) cell subsets were observed.HLA-DR+TRM andKIR+cells were clonally expanded and exhibited distinct transcriptional features, enriched for T cell activation pathways and natural killer (NK) cell-mediated cytotoxicity pathway respectively. Lastly, KIR+CD8+T cells were increased in AxSpA blood and enriched for CD45RA+CCR7-TEMRAcells.

Conclusion

Here we present the very first transcriptomic profiling of CD8+T cells in synovium tissue and highlight potential roles ofHLA-DR+TRM andKIR+cells in AxSpA pathology. This study adds novel insights to the disease mechanisms and offers new therapeutic opportunities.
RNA sequencing depth guidelines for the study of alternative splicing
Authors: Tsoy Olga , Ameling Sabine , Franzenburg Sören , Hoffmann Markus , Liv-Willuth Lina , Lee Hye Kyung , Knabl Ludwig , Furth Priscilla A. , Völker Uwe , Hennighausen Lothar , Baumbach Jan , Kacprowski Tim , List Markus
Published: October 2024

A key parameter in the experimental design of RNA-seq projects is the choice of sequencing depth. Considering a limited budget, one needs to find a tradeoff between the number of samples and the sensitivity of the analysis, particularly concerning lowly expressed genes. While previous studies have proposed a lower bound for the comprehensive analysis of differential gene expression, for the analysis of alternative splicing, it has only been proposed for human adipose tissue. However, alternative splicing differs across tissues and conditions. We analyzed publicly available and newly generated deep-sequenced paired-end RNA-seq samples (between 150 and >500 million reads, read length 50-150 bp) from human buffy coat cells and diverse sets of tissues, including gluteal subcutaneous fat, heart, and hypothalamus. Our results show that the sequencing depth typically used in published cohorts is not sufficient to comprehensively capture the landscape of alternative splicing. This motivates the use of deeper sequencing or long-read technologies in future studies. Toward this goal, we offer guidelines for choosing a suitable sequencing depth.

GRAPHICAL ABSTRACT
Fibrous Network Nature of Plant Cell Walls Enables Tunable Mechanics for Development
Authors: Chen Si , Burda Isabella , Jani Purvil , Pendrak Bex , Silberstein Meredith N. , Roeder Adrienne H.K.
Published: October 2024

During plant development, the mechanical properties of the cell walls must be tuned to regulate the growth of the cells. Cell growth involves significant stretching of the cell walls, yet little is known about the mechanical properties of cell walls under such substantial deformation, or how these mechanical properties change to regulate development. Here, we investigated the mechanical behavior of the Arabidopsis leaf epidermal cells being stretched. We found that the mechanical properties arise from the cell wall, which behaves as a fibrous network material. The epidermis exhibited a non-linear stiffening behavior that fell into three regimes. Each regime corresponded to distinct nonlinear behaviors in terms of transverse deformation (i.e., Poisson effect) and unrecoverable deformation (i.e., plasticity). Using a model, we demonstrated that the transition from reorientation and bending-dominated to stretch-dominated deformation modes of cellulose microfibrils cause these nonlinear behaviors. We found the stiffening behavior is more pronounced at later developmental stages. Finally, we show thespiral2-2mutant has anisotropic mechanical properties, likely contributing to the spiraling of leaves. Our findings reveal the fibrous network nature of cell walls gives a high degree of tunability in mechanical properties, which allows cells to adjust these properties to support proper development.
Back to the Future: Environmental genomic selection to take advantage of polygenic local adaptation
Authors: Halpin-McCormick Anna , Campbell Quinn , Negrao Sonia , Morrell Peter L , Hubner Sariel , Neyhart Jeffrey , Kantar Michael Benjamin
Published: October 2024

The genetic basis of adaptation is a fundamental question in evolutionary genetics. Environmental association analysis (EAA) and various allele frequency comparisons in genomic environmental association (GEA) have become standard approaches for investigating the genetic basis of adaptation to natural environments. While these analyses provide insight into local adaptation, they have not been widely adopted in breeding or conservation programs. This may be attributable to the difficulty in identifying the best individuals for transplantation/relocation in conservation efforts or identification of the best parents in breeding programs. To explore the use of EAA and GEA for future breeding programs, we used a cereal crop - barley (Hordeum vulgare L.) as our case-study species due to its wide adaptability to different environments and agro-ecologies, ranging from marginal and low input fields to high-productive farms. Here, we use publicly available data to conduct environmental genomic selection (EGS) on 753 landrace barley accessions using a mini-core of 31 landrace accessions and a de-novo core of 100 as the training populations. Environmental genomic selection is to environmental association analysis (EAA) what genomic selection is to genome-wide association studies (GWAS). Since local adaptation to the environment is polygenic, a whole-genome approach is likely to be more accurate for selecting for environmental adaptation. Here we show distinct genetic background and population differences and how an integrative approach coupling environmental genomic selection and species distribution modelling can help identify key parents for breeding for adaptation to specific environmental variables and geographies to minimize linkage drag.
Structural and evolutionary determinants of Argonaute function
Authors: Wallmann Arndt , Van de Pette Mathew
Published: October 2024

Members of the Argonaute protein superfamily adopt functions ranging from host-defense to mediating elaborate and multi-component post-transcriptional and epigenetic systems of control. Despite this diversity of biological roles, the Argonaute structural fold is highly conserved throughout all domains of life. This raises questions about how Argonautes evolved to adapt to this increasing complexity of function, while conserving features that are broadly shared across the phylogenetic tree.

Integrating structural, sequence, phylogenetic data and disease-related mutational data, we compiled a comprehensive study of the Argonaute evolutionary trajectory. By comparing Argonaute proteins across a diverse set of lineages and extensive evolutionary timescale, we identified universal and clade-specific sequence signatures and intra-protein contact networks that underlie the Argonaute structural fold, nucleic acid interface and protein-protein binding sites. We analyze how these features are affected by disease-related mutations and are fundamentally altered in the case of the Argonaute-like Med13 protein. With this work we gain better insights into how Argonaute function diversified in eAgos by redrawing the emergence of conserved molecular features that are associated with new biological functions.
Reverse engineering of the pattern recognition receptor FLS2 reveals key design principles of broader recognition spectra against evading flg22 epitopes
Authors: Zhang Songyuan , Liu Songyuan , Lai Hung-Fei , Caflisch Amedeo , Zipfel Cyril
Published: October 2024

In the ongoing plant-pathogen arms race, plants employ pattern recognition receptors (PRRs) to recognize pathogen-associated molecular patterns (PAMPs), while in successful pathogens, PAMPs can evolve to evade detection. Engineering PRRs to recognize evading PAMPs could potentially generate broad-spectrum and durable disease resistance. In this study, we reverse-engineered two natural FLAGELLIN SENSING 2 (FLS2) variants, VrFLS2XL and GmFLS2b, with extended recognition specificities towards evading flg22 variants. We identified minimal gain-of-function residues enabling blind FLS2s to recognize otherwise evading flg22 variants. We uncovered two strategies: (i) enhancing FLS2-flg22 interaction around flg22’s key evasion sites, and (ii) strengthening direct interaction between FLS2 and its co-receptor BAK1 to overcome weak agonistic and antagonistic flg22s, respectively. Additionally, we leveraged polymorphisms that enhance recognition through unknown mechanisms to engineer superior recognition capability. These findings offer basic design principles for PRRs with broader recognition spectra, paving the way for PRR engineering using precise gene-editing to increase disease resistance in crops.
Wax bloom dynamics onSorghum bicolorunder different environmental stresses reveal signaling modules associated with wax production
Authors: Larson Madison , Hampton Marshall , Busta Lucas
Published: October 2024

Epicuticular wax blooms are associated with improved drought resistance in many species, includingSorghum bicolor. While the role of wax in drought resistance is well known, we report new insights into how light and drought dynamically influence wax production. We investigated how wax quantity and composition are modulated over time and in response to different environmental stressors, as well as the molecular and genetic mechanisms involved in such. Gas chromatography-mass spectrometry and photographic results showed that sorghum leaf sheath wax load and composition were altered in mature plants grown under drought and simulated shade, though this phenomenon appears to vary by sorghum cultivar. We combined anin vitrowax induction protocol with GC-MS and RNA-seq measurements to identify a draft signaling pathway for wax bloom induction in sorghum. We also explored the potential of spectrophotometry to aid in monitoring wax bloom dynamics. Spec-trophotometric analysis showed primary differences in reflectance between bloom-rich and bloomless tissue surfaces in the 230-500nm range of the spectrum, corresponding to the blue color channel of photographic data. Our smartphone-based system detected significant differences in wax production between control and shade treatment groups, demonstrating its potential for candidate screening. Overall, our data suggest that wax extrusion can be rapidly modulated in response to light, occurring within days compared to the months required for the changes observed under greenhouse drought/simulated shade conditions. These results highlight the dynamic nature of wax modulation in response to varying environmental stimuli, especially light and water availability.

Significance Statement

Agricultural crops require significant freshwater for irrigation, making food security vulnerable to drought. Epicuticular wax blooms are associated with drought tolerance in many plants, includingSorghum bicolor. We investigated how environmental factors like light and drought influence wax production in sorghum. Wax production, composition, and gene expression were compared between sorghum exposed to different environmental stressors, reavealing dynamic modulation of wax production in response to environmental stress as well as signaling genes potentially involved in regulating wax production. These findings broaden our understanding of wax-related drought tolerance mechanisms, providing a foundation for future efforts to enginner crops with improved climate resilience.
Exploring the Efficiency of Deep Graph Neural Networks for RNA Secondary Structure Prediction
Authors: Saon Md. Sharear , Boehm Kevin , Fu Grace , Hou Ian , Yu Jerry , Znosko Brent M. , Hou Jie
Published: October 2024

Ribonucleic acid (RNA) plays a vital role in various biological processes and forms intricate secondary and tertiary structures associated with its functions. Predicting RNA secondary structures is essential for understanding the functional and regulatory roles of RNA molecules in biological processes. Traditional free-energy-based methods for predicting these structures often fail to capture complex interactions and long-range dependencies within RNA sequences. Recent advancements in machine learning, particularly with graph neural networks (GNNs), have shown promise in enhancing the ability to model the relationships between molecular sequences and their structures. This work specifically explores the efficacy of various GNN architectures in modeling RNA secondary structure. Through benchmarking the GNN methods against traditional energy-based models on standard datasets, our analysis demonstrates that GNN models improves traditional methods, offering a robust framework for accurate RNA structure prediction.
Real-time genomic characterization of pediatric acute leukemia using adaptive sampling
Authors: Geyer Julie , Opoku Kofi B. , Lin John , Ramkissoon Lori , Mullighan Charles , Bhakta Nickhill , Alexander Thomas B. , Wang Jeremy R.
Published: October 2024

Effective treatment of pediatric acute leukemia is dependent on accurate genomic classification, typically derived from a combination of multiple time-consuming and costly techniques such as flow cytometry, fluorescencein situhybridization (FISH), karyotype analysis, targeted PCR, and microarrays (Arber et al., 2016; Iacobucci & Mullighan, 2017; Narayanan & Weinberg, 2020). We investigated the feasibility of a comprehensive single-assay classification approach using long-read sequencing, with real-time genome target enrichment, to classify chromosomal abnormalities and structural variants characteristic of acute leukemia. We performed whole genome sequencing on DNA from diagnostic peripheral blood or bone marrow for 57 pediatric acute leukemia cases with diverse genomic subtypes. We demonstrated the characterization of known, clinically relevant karyotype abnormalities and structural variants concordant with standard-of-care clinical testing. Subtype-defining genomic alterations were identified in all cases following a maximum of forty-eight hours of sequencing. In 18 cases, we performed real-time analysis – concurrent with sequencing – and identified the driving alteration in as little as fifteen minutes (for karyotype) or up to six hours (for complex structural variants). Whole genome nanopore sequencing with adaptive sampling has the potential to provide genomic classification of acute leukemia specimens with reduced cost and turnaround time compared to the current standard of care.
New insights into past and future invasion ofDrosophila suzukiiusing novel genomic resources and statistical methods to combine individual and pool sequencing data
Authors: Camus Louise , Rode Nicolas , Serga Svitlana , Loiseau Anne , Chen Xiao , Iampietro Carole , Kenis Marc , Marande William , Mensch Julián , Parinello Hugues , Savić Veselinović Marija , Valière Sophie , Zhang Jinping , Estoup Arnaud , Boitard Simon , Gautier Mathieu
Published: October 2024

Climate change and globalization are accelerating biological invasions, highlighting the urgent need to understand adaptation mechanisms in invaded environments to improve management strategies. Genomic data can provide insights into the adaptation of invasive species through Genotype-Environment Association (GEA) studies, identifying genes and biological processes associated with invasion success, and more globally to estimate genetic (mal)adaptation to new environments by calculating Genomic Offset (GO) statistics. In this study, we investigate genetic adaptation in the invasive crop pestDrosophila suzukiiusing novel genomic resources and statistical methods. We rely on a new chromosome-level genome assembly and a dataset representing 36 populations, combining both publicly available and newly generated pooled and individual sequencing data, which are analyzed using an enhanced version of the BayPasssoftware, tailored for such hybrid datasets. We identify a limited number of genomic regions associated with invasion success, supporting the hypothesis of a polygenic architecture of the underlying adaptive traits. Using a GEA incorporating 28 environmental covariates, we further estimate GO between source environments and invaded areas to gain insight into the adaptive challenges faced byD. suzukiiduring past invasions. Reciprocally, we estimate GO between putative source environments and geographic areas that have not yet been invaded to predict regions at risk for potential future invasions. Finally, we used GO calculation to identify high risk regions from which pre-adapted populations could likely originate. Our results suggest that the adaptive challenge forD. suzukiipopulations to invade their current major invasion range was limited. We also identified uninvaded regions (in Africa, South America, and Australia) as being at high risk of future invasion. While further sampling and more extensive individual sequencing could refine these conclusions, our study provides important insights intoD. suzukiiadaptation and offers a generic and operational population genomics framework for studying and predicting biological invasions that can be applied to diverse species.
Knockdown proteomics reveals USP7 as a regulator of cell-cell adhesion in colorectal cancer via AJUBA
Authors: Al-Eidan Ahood , Draper Ben , Wang Siyuan , Coke Brandon , Skipp Paul , Wang Yihua , Ewing Rob M.
Published: October 2024

Ubiquitin-specific protease 7 (USP7) is implicated in many cancers including colorectal cancer in which it regulates cellular pathways such as Wnt signalling and the P53-MDM2 pathway. With the discovery of small-molecule inhibitors, USP7 has also become a promising target for cancer therapy, and therefore systematically identifying USP7 deubiquitinase interaction partners and substrates has become an important goal. In this study, we selected a colorectal cancer cell model that is highly dependent on USP7 and in which USP7 knockdown significantly inhibited colorectal cancer cell viability, colony formation, and cell-cell adhesion. We then used inducible knockdown of USP7 followed by LC-MS/MS to quantify USP7 dependent proteins. We identified the Ajuba LIM domain protein as an interacting partner of USP7 through co-IP, its substantially reduced protein levels in response to USP7 knockdown, and its sensitivity to the specific USP7 inhibitor FT671. The Ajuba protein has been shown to have oncogenic functions in colorectal and other tumours, including regulation of cell-cell adhesion. We show that both knockdown of USP7 or Ajuba results in a substantial reduction of cell-cell adhesion, with concomitant effects on other proteins associated with adherens junctions. Our findings underlie the role of USP7 in colorectal cancer through its protein interaction networks and show that the Ajuba protein is a component of USP7 protein networks present in colorectal cancer.
EphA2 and Phosphoantigen-Mediated Selective Killing of Medulloblastoma by γδT Cells Preserves Neuronal and Stem Cell Integrity
Authors: Boutin Lola , Liu Mingzhi , Merville Julie Déchanet , Bedoya-Reina Oscar , Wilhelm Margareta T
Published: October 2024

Medulloblastoma (MB) is a pediatric brain tumor that develops in the cerebellum, representing one of the most common malignant brain cancers in children. Standard treatment includes surgery, chemotherapy, and radiation, but despite a 5-year survival rate of approximately 70%, these therapies often lead to significant neurological damage in the developing brain. This underscores the urgent need for less toxic, more effective therapeutic alternatives. Recent advancements in cancer immunotherapy, including immune checkpoint inhibitors and CAR-T cell therapy, have revolutionized cancer treatment. One promising avenue is the use of Gamma Delta (γδ)T cells, a unique T cell population with potential advantages such as non-alloreactivity, potent tumor cell lysis, and broad antigen recognition. However, their capacity to recognize and target MB cells remains underexplored. To investigate the therapeutic potential of γδT cells against MB, we analyzed the proportion and status of MB-infiltrated γδT cells within patient datasets. We next investigated the expression of γδT cell ligands on MB cells and identified EphA2 receptor and the phosphoantigen/Butyrophilin complex as key ligands, activating Vγ9Vδ1 and Vγ9Vδ2 T cells, respectively, leading to significant MB cell lysis in both monolayer and spheroid models. Importantly, preliminary safety data showed that γδT cells did not target differentiated neurons or neuroepithelial stem cells derived from induced pluripotent stem cells, underscoring the selectivity and safety of this approach. In conclusion, γδT cells trigger an efficient and specific killing of MB, and would offer a promising novel therapeutic strategy.

Key messages

Medulloblastoma patients often experience significant long-term side effects from current standard treatments. Immunotherapy has emerged as a promising alternative to conventional therapeutic approaches. In our study, we demonstrated that γδT cells can efficiently and specifically target medulloblastoma cells without causing harm to healthy neuronal tissue. These findings suggest that γδ T cell therapy may provide therapeutic benefits while potentially reducing treatment-related toxicity in medulloblastoma patients.
Essential tremor with tau pathology features seeds indistinguishable in conformation from Alzheimer’s disease and primary age-related tauopathy
Authors: Saez-Calveras Nil , Vaquer-Alicea Jaime , White Charles L. , Tak Yogesh , Cosentino Stephanie , Faust Phyllis L. , Louis Elan D. , Diamond Marc I.
Published: October 2024

Neurodegenerative tauopathies are characterized by the deposition of distinct fibrillar tau assemblies whose rigid core structures correlate with defined neuropathological phenotypes. Essential tremor (ET) is a progressive neurological disease disease that, in some cases, is associated with cognitive impairment and tau accumulation.. Consequently, we explored the tau assembly conformation in ET patients with tau pathology using cytometry-based tau biosensor assays. These assays quantify tau prion seeding activity present in brain homogenates based on conversion of intracellular tau-fluorescent protein fusions from a soluble to an aggregated state. Prions exhibit seeding barriers, whereby a specific assembly structure cannot serve as a template for a native monomer if the amino acids are not compatible. We recently exploited the tau prion species barrier to define tauopathies by systematically substituting alanine (Ala) in the tau monomer and measuring its incorporation into seeded aggregates within biosensor cells. The Ala scan precisely classified the conformation of tau seeds from diverse tauopathies. We next studied 18 ET patient brains with tau pathology. Only one case had concurrent high amyloid-β plaque pathology consistent with Alzheimer’s disease (AD). We detected robust tau seeding activity in 9 (50%) of the patients. This predominantly localized to the temporal pole and temporal cortex. We examined 8 ET cases with the Ala scan and determined that the amino acid requirements for tau monomer incorporation into aggregates seeded from these ET brain homogenates were identical to those of AD and primary age-related tauopathy (PART), and completely distinct from other tauopathies such as corticobasal degeneration, chronic traumatic encephalopathy, and progressive supranuclear palsy. Based on these studies, tau assembly cores in a pathologically confined subset of ET cases with high tau pathology are identical to AD and PART. This could facilitate more precise diagnosis and therapy for ET patients with cognitive impairment.
Maximum vertical height during wing flapping of laying hens captured with a depth camera
Authors: Grebey Tessa , Bongiorno Valentina , Han Junjie , Steibel Juan , Siegford Janice M.
Published: October 2024

Cage-free housing systems for laying hens, and their accompanying guidelines, legislation, and audits, are becoming more common around the world. Cage-free regulations often specify requirements for floor space and cage height, but the availability of three-dimensional space can vary depending on system configurations. Little research has looked at how much vertical space a hen occupies while flapping her wings, which is arguably her most space-intensive behavior. Therefore, the objective of this study was to use a depth sensing camera to measure the maximum vertical height hens reach when wing flapping without physical obstructions. Twenty-eight individually caged Hy-line W36 hens at 45 weeks of age were evaluated. A ceiling-mounted depth camera was centered above a test pen and calibrated prior to collecting data. During testing, one hen at a time was placed in the test pen and recorded flapping her wings. From depth footage, the minimum distance between pixels was obtained for each frame, and we computed the maximum vertical height reached by each hen. Results for vertical space used during a wing flapping event showed that hens reached a maximum height of 51.0 ± 4.7 cm. No physical measures correlated with maximum height obtained from the depth camera (P>0.05). Hens in this study were from a single strain, were old enough to have keel damage, and were cage-reared and housed, preventing us from generalizing the results too far. However, depth cameras provide a useful approach to measure how much space laying hens of varying strains, ages, and rearing/housing methods need to perform dynamic behaviors.
A noncanonical glycoprotein H complex enhances cytomegalovirus entry
Authors: Norris Michael J. , Henderson Lauren A. , Siddiquey Mohammed N.A. , Yin Jieyun , Yoo Kwangsun , Brunel Simon , Saphire Erica Ollmann , Benedict Chris A. , Kamil Jeremy P.
Published: October 2024

Human cytomegalovirus (HCMV) causes severe birth defects, lifelong health complications, and $4 billion in annual costs in the United States alone. A major challenge in vaccine design is the incomplete understanding of the diverse protein complexes the virus uses to infect cells. InHerpesviridae, the gH/gL glycoprotein heterodimer is expected to be a basal element of virion cell entry machinery. For HCMV, gH/gL forms a “trimer” with gO and a “pentamer” with UL128, UL130, and UL131A, with each complex binding distinct receptors to enter varied cell types. Here, we reveal a third glycoprotein complex, abundant in HCMV virions, which significantly enhances infection of endothelial cells. In this “3-mer” complex, gH, without gL, associates with UL116 and UL141, an immunoevasin previously known to function in an intracellular role. Cryo-EM reveals the virion-surface 3-mer is structurally unique amongHerpesviridaegH complexes, with gH-only scaffolding, UL141-mediated dimerization and a heavily glycosylated UL116 cap. Given that antibodies directed at gH and UL141 each can restrict HCMV replication, our work highlights this virion surface complex as a new target for vaccines and antiviral therapies.
The food grade bacteriumLactobacillus helveticus VEL12193promotes autophagy by releasing membrane vesicles
Authors: Bringer Marie-Agnès , Al Azzaz Jana , Buteau Bénédicte , Proukhnitzky Lil , Aumeunier Amaury , Manceau Simon , Bermúdez-Humarán Luis G. , Florian Chain F , Daniel Catherine , Jacquin Elise , Acar Niyazi , Rieu Aurélie , Lapaquette Pierre
Published: October 2024

Autophagy-related processes, including canonical macroautophagy, are crucial for maintaining cellular homeostasis in eukaryotic organisms. Alterations or reduced activity of these processes have been strongly linked to a broad range of human diseases including inflammatory bowel disease (IBD) and age-related diseases such as age-related macular degeneration - a disease that affect the central area of the retina. In contrast, long-term autophagy stimulation appears to be safe and to extend lifespan in model organisms such as mice. Thus, enhancing autophagy represents a promising strategy for promoting healthy aging. Several studies indicate that the gut microbiota can influence host autophagy at the gut mucosa but also in peripheral organs, and some microbial metabolites have been identified as autophagy modulators. In this study, we studied the capacity of bacterial species commonly used in food fermentation (ferments) or health (probiotics) to modulate host autophagy byin vitroandin vivoapproaches.In vitroscreening of a library of 11 bacterial strains revealed a strain-dependent ability of lactobacilli and bifidobacteria to stimulate autophagy in human epithelial cells. TheLactobacillus helveticusstrain VEL12193, isolated from cheese, emerged as the most effective inducer of autophagy.In vivoexperiment using mice showed that long-term dietary supplementation withL. helveticusVEL12193 was associated with stimulation of autophagy in the gut mucosa and retina. We identifiedL. helveticus-derived membrane vesicles (MVs) as a bacterial component involved in bacterial-induced autophagy in epithelial and immune cells. Moreover,in vitro, we demonstrated thatL. helveticusVEL12193 possesses immunomodulatory properties in macrophages, as well as in the gut mucosa of a preclinical mouse model of IBD. With this study we provide robust proof of concept that ferments/probiotics can stimulate autophagy at the organism scale and that this phenotype involved MVs. In addition, we identifyL. helveticusVEL12193 as a candidate strain of interest for the design of healthy-aging strategies.
In vitroactivity of hydroxychloroquine in combination with antibiotics against intracellular uropathogenicEscherichia coli
Authors: Pargny V. , Vautrin N. , Ribet D. , Minlong O. , Caron F. , Pestel-Caron M. , Alexandre K.
Published: October 2024

Background

Two pathophysiological concepts may explain recurrent UTI: a reinfection by a bacterial strain from the digestive microbiota or a relapse fromEscherichia colipersisting within the superficial urothelial cells as intracellular bacterial communities (IBC). Hydroxychloroquine (HCQ)-antibiotic combination is effective against intracellular adherent-invasiveE. coliisolated from patients with Crohn’s disease. We hypothesized that HCQ may enhanced antibiotic efficacy againstE. coliIBC.

Methods

UTI89 reference strain and two clinicalE. colistrains forming IBCs (VITALE#2157, VITALE#2206) were used in this study. MIC, MBC and time killing curves (4xMIC) were performed for AZYTHROMYCIN (AZT), CIPROFLOXACIN (CIP), DOXYCYCLINE (DC), FOSFMOMYCIN (FF) and HCQ.In vitroactivity of antibiotics alone and combined with HCQ was evaluated on intracellular bacterial survival assay using a model of urothelium cells (HTB-9).

Results

Time-killing curves showed that CIP has a bactericidal activity at H6 (-4.6 log10CFU/mL) with regrowth at H24 against 2157, and a bactericidal activity at H6 without regrowth at H24 against 2206 (-3.3 log10CFU/mL) and UTI89 (-3.4 log10CFU/mL); DC, AZT and FF demonstrated bacteriostatic activity at H24 regardless of the strain. We observed a significant decrease in the number of intracellular bacteria at H42 with CIP (-1.83 log10/ 106cells). DC, FF, and AZT exposure did not reduce IBC formation at H42 (P>0.05). IBC formation after HCQ-antibiotic combination exposure was not significantly different (P>0.05) from antibiotic exposure alone, regardless of the antibiotic or strain studied.

Conclusions

In conclusion, HCQ exposure does not enhance antibiotics activity against intracellular uropathogenicE. coli.

Highlights

Using anin vitromodel of superficial urothelium monolayer, we observed a significant decrease in intracellular uropathogenicEscherichia coliin response to ciprofloxacin exposure.

Hydroxychloroquine exposure does not enhance antibiotics activity against intracellular uropathogenicEscherichia coli.
A family of Tn7-like transposons evolved to target CRISPR repeats
Authors: Chacon Machado Laura , Peters Joseph E.
Published: October 2024

Tn7 family transposons are mobile genetic elements known for precise target site selection, with some co-opting CRISPR-Cas systems for RNA-guided transposition. We identified a novel group of Tn7-like transposons in Cyanobacteria that preferentially target CRISPR arrays, suggesting a new functional interaction between these elements and CRISPR-Cas systems. Using bioinformatics tools, we characterized their phylogeny, target specificity, and sub-specialization. The array-targeting elements are phylogenetically close to tRNA-targeting elements. The distinct target preference coincides with loss of a C-terminal region in the TnsD protein which is responsible for recognizing target sites when compared to closely related elements. Notably, elements are found integrated into a fixed position within CRISPR spacer regions, a behavior that might minimize negative impacts on the host defense system. These transposons were identified in both plasmid and genomic CRISPR arrays, indicating that their preferred target provides a means for both safe insertion in the host chromosome and a mechanism for dissemination. Attempts to reconstitute these elements inE. coliwere unsuccessful, indicating possible dependence on native host factors. Our findings expand the diversity of interactions between Tn7-like transposons and CRISPR systems.
Surfactin acceleratesBacillus subtilispellicle biofilm development
Authors: Stannius Rune Overlund , Fusco Sarah , Cowled Michael , Kovács Ákos T.
Published: October 2024

Surfactin is a biosurfactant produced by manyB. subtilisstrains with a wide variety of functions from lowering surface tension to allowing motility of bacterial swarms, acting as a signaling molecule, and even exhibiting antimicrobial activities. However, the impact of surfactin during biofilm formation has been debated with variable findings between studies depending on the experimental conditions.

B. subtilisis known to form biofilms at the solid-air, the solid-medium, and the liquid-air interfaces, the latter of which is known as a pellicle biofilm. Pellicle formation is a complex process requiring coordinated movement to the liquid-air interface and subsequent cooperative production of biofilm matrix components to allow robust pellicle biofilm formation. This makes pellicle formation a promising model system for assaying factors in biofilm formation and regulation.

Here, we assayed the influence of surfactin and additional metabolites on the timing of pellicle biofilm formation. Using of time-lapse imaging, we assayed pellicle formation timing in 12B. subtilisisolates and found that one, MB9_B4, was significantly delayed in pellicle formation by approximately 10 hours. MB9_B4 was previously noted to lack robust surfactin production. Indeed, deletion of surfactin synthesis in the other isolates delayed pellicle formation. Further, pellicle delay was rescued by addition of exogeneous surfactin and spent media from mature pellicles. Testing reporters of biofilm-related gene expression revealed that induction of pellicle formation was caused by a combination of increased gene expression of one of the biofilm components and promotion of growth. Intriguingly, spent media of surfactin mutant strains were also able to stimulate pellicle formation, indicating possible additional metabolites also influence the timing of pellicle development.
Independent control of neurogenesis and dorsoventral patterning by NKX2-2
Authors: Jang Sumin , Abarinov Elena , Dobkin Julie , Wichterle Hynek
Published: October 2024

Human neurogenesis is disproportionately protracted, lasting >10 times longer than in mouse, allowing neural progenitors to undergo more rounds of self-renewing cell divisions and generate larger neuronal populations. In the human spinal cord, expansion of the motor neuron lineage is achieved through a newly evolved progenitor domain called vpMN (ventral motor neuron progenitor) that uniquely extends and expands motor neurogenesis. This behavior of vpMNs is controlled by transcription factor NKX2-2, which in vpMNs is co-expressed with classical motor neuron progenitor (pMN) marker OLIG2. In this study, we sought to determine the molecular basis of NKX2-2-mediated extension and expansion of motor neurogenesis. We found that NKX2-2 represses proneural geneNEUROG2by two distinct, Notch-independent mechanisms that are respectively apparent in rodent and human spinal progenitors: in rodents (and chick), NKX2-2 repressesOlig2and the motor neuron lineage through its tinman domain, leading to loss ofNeurog2expression. In human vpMNs, however, NKX2-2 repressesNEUROG2but notOLIG2, thereby allowing motor neurogenesis to proceed, albeit in a delayed and protracted manner. Interestingly, we found that ectopic expression of tinman-mutantNkx2-2in mouse pMNs phenocopies human vpMNs, repressingNeurog2but notOlig2, and leading to delayed and protracted motor neurogenesis. Our studies identify a Notch- and tinman-independent mode ofNkx2-2-mediatedNeurog2repression that is observed in human spinal progenitors, but is normally masked in rodents and chicks due toNkx2-2’s tinman-dependent repression ofOlig2.
Robust quantification of cellular mechanics using optical tweezers
Authors: Rodenburg Wessel S. , Ebben Sven F.A. , Eeftens Jorine M.
Published: October 2024

Mechanical properties of cells are closely related to function and play a crucial role in many cellular processes, including migration, differentiation, and cell fate determination. Numerous methods have been developed to assess cell mechanics under various conditions, but they often lack accuracy on biologically relevant piconewton-range forces, or have limited control over the applied force. Here, we use optically-trapped polystyrene beads to accurately apply piconewton-range forces to adherent and suspended cells. We precisely apply a constant force to cells by means of a force-feedback system, allowing for quantification of deformation, cell stiffness and creep response from a single measurement. Using drug-induced perturbations of the cytoskeleton, we show that this approach is sensitive to detecting changes in cellular mechanical properties. Collectively, we provide a framework for using optical tweezers to apply highly accurate forces to adherent and suspended cells, and describe straightforward metrics to quantify cellular mechanical properties.
From data silos to seamless integration and coordination: a data-asset centric approach to smart hospital facility management
Authors: Li Lingzhi , Jiang Shilong , Yuan Jingfeng , Zhang Lei , Xu Xiaoxiao , Wang Jing , Zhou Yilun , Li Yunlong , Xu Jin
Published: October 2024

Purpose

Existing hospital building operations involve numerous information technology applications and complex building systems; therefore, an intelligent facility management (FM) platform is required to ensure their continuous operation. To address the persistent issues of data silos, inefficient data interoperability, and workflow incoordination that have been identified in the current body of FM practice and literature, the present study develops a data-asset (DA) centric FM platform specifically designed for hospital buildings.

Design/methodology/approach

This study proposes a semi-customized approach to develop the DA-centric FM platform for hospital buildings. To elucidate the precise function requirements of the hospital FM platform, focus group interviews are employed. By seamlessly integrating the as-built BIM model, IoT sensor data and FM workflow data, the BIM-based DA model with a data transfer mechanism is developed. The development of the FM platform with function modules in a case study is guided by a five-tier architecture and the coordination theory (CT). The case study provides an in-depth introduction to the applications of DA management, space management and maintenance management modules.

Findings

The capabilities of the developed DA-centric hospital FM platform are validated through the case application and user satisfaction survey, which assess data quality, automation level, operation efficiency, flexibility and functionality. For hospital FM activities, this DA-centric FM platform realizes data integration and seamless transformation, optimizes workflow coordination and enhances operation performance.

Originality/value

The initial scholarly contribution is the establishment of the BIM-based DA model, which serves as the data middle platform for continuous data integration, transmission and sharing within the FM platform. Subsequently, under the guidance of the CT, the business process of function modules is designed, improving the intra-module and inter-module workflow coordination. The developed DA-centric FM system along with its performance benchmarking application, assists facility managers and decision-makers in implementing smart operations for hospital buildings and achieving the management goals of safety, efficiency, energy savings and convenience.
Relational antecedents of sharing and not sharing knowledge: a configurational approach
Authors: Rudawska Aleksandra , Sławik Anna
Published: October 2024

Purpose

Knowledge sharing within organizations has significant benefits for group and organizational performance. This study aims to identify the combinations of individual and relational factors that influence high- and low-intensity knowledge sharing among workers using the ability-motivation-opportunities (AMO) framework.

Design/methodology/approach

This research adopts a qualitative, set-theoretic approach, using fuzzy set qualitative comparative analysis (fsQCA) to analyse data collected from knowledge workers in an international corporation.

Findings

Our findings show that knowledge sharing is fundamentally relational, meaning that the quality and history of interaction with co-workers affect the intensity of knowledge-sharing behaviour. All AMO dimensions prove important for sharing, although some of them can substitute one another. However, if there is a lack of ability and opportunity, employees will not share knowledge even if they are motivated by reciprocity.

Practical implications

The results offer human resources and project management practice alternative combinations of individual and relational factors that can be used to streamline knowledge sharing, emphasizing the need to invest in building relationships among co-workers.

Originality/value

This study contributes to the literature by identifying configurations of core and peripheral conditions pertaining to abilities, motivation and opportunities that can facilitate or constrain knowledge-giving.