bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amyloplasts are necessary for full gravitropism in thallus ofMarchantia polymorpha
Authors: Hashimoto-Sugimoto Mimi , Norizuki Takuya , Segami Shoji , Ohta Yusaku , Suetsugu Noriyuki , Ueda Takashi , Morita Miyo Terao 
Published: November 2024

AbstractGravitropism is a response in which plants sense gravity and determine the direction of organ growth and development. This trait is important for adaptation in land plants. The molecular mechanisms of gravitropism have been studied mainly in flowering plants, but there is limited research on other organisms. In this study, we examined the gravitropic response of the liverwortMarchantia polymorpha, a model for investigating the evolution of land plants. We found the tips of the thallus extend upward and form several straight narrow structures in the dark. These growth directions were always in the opposite direction of gravity, and clinostat treatment disrupted them. The parenchymatous cells in the narrow structures contained amyloplasts, and the sedimentation of the amyloplasts preceded the gravitropic curvature, suggesting their role as statoliths. The starchless mutants, Mppgm1 andMpaps1were generated, and an abnormal direction of growth was observed in the narrow structures, but they tended to elongate upward. These observations indicate that although amyloplasts are required for complete gravitropism, plants can sense gravity without well-developed amyloplasts. These results suggest that land plants use amyloplasts as statoliths but also have amyloplast-independent mechanisms of gravitropism. These results suggest that land plants use amyloplasts as statoliths but also have amyloplast-independent mechanisms of gravitropism.HighlightInM. polymorpha,amyloplasts act as statoliths in parenchyma cells and are important in gravitropism but it was not completely lost without starch granules.
Assessment of neurobehavioural traits under axenic conditions: an approach for multiple longitudinal analyses in the same mouse
Authors: Rutsch Andrina , Iachizzi Monica , Kirundi Jorum , Kantsjö Johan B. , Planchette Arielle L. , Müller Terry , Schmitz Werner , Radenovic Aleksandra , Doenlen Raphaël , de Agüero Mercedes Gomez , Ronchi Francesca 
Published: November 2024

AbstractThe gut-microbiota-brain axis influences neuroinflammation, neural development and behaviour such as sociability, memory and anxiety. To study these traitsin vivo, especially during development or disease, it is crucial to analyse them over time and with multiple analyses in the same animal. With a growing understanding of the role of specific bacteria in neurodegenerative disease and behaviour, the demand for gnotobiotic mouse models has increased. However, maintaining stable hygienic conditions during behavioural testing is challenging, as exposure to conventional environments can alter the hygienic status of mice and affect behaviour. We established protocols to perform behavioural tests assessing memory, anxiety, exploration, learning and recognition under axenic conditions using flexible film isolators. Our study compared the behaviour of germ-free mice with mice carrying a defined minimal or moderately diverse microbiota. The results showed no effect of the microbiota on short- and long-term memory or novel object recognition. However, we showed for the first time that mice colonised with defined commensal bacteria exhibited more anxiety-like behaviour than germ-free mice. In addition, we showed that microbiota complexity is important, as only mice colonised with moderately diverse microbiota exhibited anxiety-like behaviour, allowing us to disentangle the contribution of specific microbial species or community interactions to this phenotype. This phenotype correlated with differences in hippocampal and serum metabolic profiles between colonised and germ-free mice. We propose a novel approach to study rodent behaviour at different physiological and pathological stages in their life without compromising hygiene, thus promoting the refinement and reduction of mice used in experiments.
Astrocyte-specific secretome profiling reveals its correlation with neurological disorders
Authors: Liu Jie , Gao Jing , Guo Lin , Ma Guoming , Guan Mingfeng , Xia Congcong , He Jia , Yang Yufang , Wu Yi , Xu Jun , Xiong Liulin , Yu Chang-Yin , Pei Gang , Zhao Jian , He Jianchen , Zhang Yaoyang , Wang Wenyuan 
Published: November 2024

ABSTRACTSecreted proteins mediate intercellular communication throughout the lives of multicellular organisms. However, due to the lack of new technology for secreted protein capturing, the progress of “secretomics’’ lags behind. Here, we report a two-step secretome enrichment method (tsSEM) combining unnatural amino acid labeling and click chemistry-based biorthogonal reaction, which enablesin vitrosecretome profiling in the presence of serum. Using this novel method, we systematically investigated the secretome of human iPSCs-derived astrocytes (iAst) in different disease models and identified a panel of astrocyte-secreted proteins that are responsible for its non-cell autonomous toxicity under disease conditions. Furthermore, we validated two astrocytes-derived novel neurotrophic proteins, FAM3C and KITLG, which we identified from disease models, and found that they could boost neurite outgrowth, protect neurons, and promote neural progenitor proliferation. Our study highlights the utility of secretome profiling of iAst and demonstrates its applications in disease study and target identification and validation in drug development.
Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding
Authors: Paldi Flora , Szalay Michael F , Di Stefano Marco , Jost Daniel , Reboul Hadrien , Cavalli Giacomo 
Published: November 2024

AbstractEpigenetic memory enables the stable propagation of gene expression patterns in response to transient developmental and environmental stimuli. Although three-dimensional (3D) organisation is emerging as a key regulator of genome function, it is unknown whether it contributes to cellular memory. Here, we establish that acute perturbation of the epigenome can induce cellular memory of gene expression in mouse embryonic stem cells (mESCs). Specifically, we uncover how a pulse of histone deacetylase inhibition translates to changes in histone acetylation and methylation, as well as global and local genome folding. While most epigenomic and transcriptional changes are readily reversible once the perturbation is removed, genome architecture partially maintains its perturbed conformation. This is significant, as a second transient pulse of hyperacetylation induces continued gene expression deregulation at hundreds of loci. Using ultra-deep Micro-C, we associate memory of gene expression with enhancer-promoter contacts and repressive chromatin topology mediated by Polycomb. These results demonstrate how cells are able to record a transient stress in their 3D genome architecture, enabling them to respond more robustly in a second bout of the same perturbation.
Multiplexed PCR to measurein situgrowth rates of uropathogenicE. coliduring experimental urinary tract infection
Authors: Paudel Santosh , Severin Geoffrey B. , Pirani Ali , Snitkin Evan S. , Mobley Harry L.T. 
Published: November 2024

AbstractMeasuring bacterial growth ratesin vitrois routine, however, determining growth rates during infection in host has been more challenging. Peak-to-trough ratio (PTR) is a technique for studying microbial growth dynamics, calculated using the ratio of replication origin (ori) copies to that of the terminus (ter), as originally defined by whole genome sequencing (WGS). WGS presents significant challenges in terms of expense and data analysis complexity due to the presence of host DNA in the samples. Here, we used multiplexed PCR with fluorescent probes to estimate bacterial growth rates based on the abundance ofori– andter-adjacent loci, without the need for WGS. We establish the utility of this approach by comparing growth rates of the uropathogenicEscherichia coli(UPEC) strain HM86 by WGS (PTR) and qPCR to measure the equivalentori:ter(O:TPCR). We found that PTR and O:TPCRwere highly correlated and that O:TPCRreliably predicted growth rates calculated by conventional methods. O:TPCRwas then used to calculate thein situ E. coligrowth rates in urine, bladder, and kidneys collected over the course of a week from a murine model of urinary tract infection (UTI). These analyses revealed that growth rate of UPEC strains gradually increased during the early stages of infection (0–6h), followed by a slow decrease in growth rates during later time points (1-7 days). This rapid and convenient method provides valuable insights into bacterial growth dynamics during infection and can be applied to other bacterial species in both animal models and clinical infections.ImportanceAccurately measuring bacterial growth rates in the host, which plays a crucial role in determining the success of pathogens in establishing infections, poses significant challenges. To address this, bacterial replication rate has been measured as a proxy for growth rate estimation. While whole genome sequencing (WGS) has been used for this purpose, it comes with drawbacks such as high costs and difficulties in analyzing bacterial sequences due to the overwhelming presence of host DNA. In this study, we validate a more accessible PCR-based approach compared to the established WGS method and confirmed the reliability of our PCR-based technique. We then applied it to measure the growth rate ofEscherichia coliduring an experimental urinary tract infection in a mouse model. This study provides a cost-effective and efficient alternative to WGS for studying bacterial replication dynamics during infection, potentially offering new insights into pathogen behavior and host-microbe interactions.
Machine Learning Identifies Genes Linked to Neurological Disorders Induced by Equine Encephalitis viruses (EEV), Traumatic Brain Injuries (TBI), and Organophosphorus nerve agents (OPNA)
Authors: Yin Liduo , VanderGiessen Morgen , Kumar Vinoth , Conacher Benjamin , Chao Po-Chien Haku , Theus Michelle , Johnson Erik , Kehn-Hall Kylene , Wu Xiaowei , Xie Hehuang 
Published: November 2024

AbstractVenezuelan, eastern, and western equine encephalitis viruses (collectively referred to as equine encephalitis viruses---EEV) cause serious neurological diseases and are a significant threat to the civilian population and the warfighter. Likewise, organophosphorus nerve agents (OPNA) are highly toxic chemicals that pose serious health threats of neurological deficits to both military and civilian personnel around the world. Consequently, only a select few approved research groups are permitted to study these dangerous chemical and biological warfare agents. This has created a significant gap in our scientific understanding of the mechanisms underlying neurological diseases. Valuable insights may be gleaned by drawing parallels to other extensively researched neuropathologies, such as traumatic brain injuries (TBI). By examining combined gene expression profiles, common and unique molecular characteristics may be discovered, providing new insights into medical countermeasures (MCMs) for TBI, EEV infection and OPNA neuropathologies and sequelae. In this study, we collected transcriptomic datasets for neurological disorders caused by TBI, EEV, and OPNA injury, and implemented a framework to normalize and integrate gene expression datasets derived from various platforms. Effective machine learning approaches were developed to identify critical genes that are associated, either shared among the three neuropathologies or to either TBI, EEV, and OPNA. With the aid of deep neural networks, we were able to extract important association signals for accurate prediction of different neurological disorders by using integrated gene expression datasets of VEEV, OPNA, and TBI samples. Gene ontology and pathway analyses further identified neuropathologic features with specific gene product attributes and functions, shedding light on the fundamental biology of these neurological disorders. Collectively, we highlight a workflow to analyze published transcriptomic data using machine learning, which can be used for both identification of gene biomarkers that are unique to specific neurological conditions, as well as genes shared across multiple neuropathologies. These shared genes could serve as potential neuroprotective drug targets for conditions like EEV, TBI, and OPNA.
Elevated EGR1 Binding at Enhancers in Excitatory Neurons Correlates with Neuronal Subtype-Specific Epigenetic Regulation
Authors: Yin Liduo , Xu Xiguang , Conacher Benjamin , Lin Yu , Carrillo Gabriela L. , Cun Yupeng , Fox Michael A. , Lu Xuemei , Xie Hehuang 
Published: November 2024

AbstractBrain development and neuronal cell specification are accompanied with epigenetic changes to achieve diverse gene expression regulation. Interacting with cell-type specific epigenetic marks, transcription factors bind to different sets of cis-regulatory elements in different types of cells. Currently, it remains largely unclear how cell-type specific gene regulation is achieved for neurons. In this study, we generated epigenetic maps to perform comparative histone modification analysis between excitatory and inhibitory neurons. We found that neuronal cell-type specific histone modifications are enriched in super enhancer regions containing abundant EGR1 motifs. Further CUT&RUN data validated that more EGR1 binding sites can be detected in excitatory neurons and primarily located in enhancers. Integrative analysis revealed that EGR1 binding is strongly correlated with various epigenetic markers for open chromatin regions and associated with distinct gene pathways with neuronal subtype-specific functions. In inhibitory neurons, the majority of genomic regions hosting EGR1 binding sites become accessible at early embryonic stages. In contrast, the super enhancers in excitatory neurons hosting EGR1 binding sites gained their accessibility during postnatal stages. This study highlights the significance of transcription factor binding to enhancer regions, which may play a crucial role in establishing cell-type specific gene regulation in neurons.
Striped-phase germanene confirmed by photoemission final-state effect
Authors: Chen Ting-Yu , Chen Chin-Hsuan , Mikolas David , Chiniwar Santosh , Huang Angus , Lin Chung-Huang , Cheng Cheng-Maw , Komori Fumio , Matsuda Iwao , Mou Chung-Yu , Jeng Horng-Tay , Pai Woei Wu , Tang S.-J. 
Published: November 2024

The formation of germanene on Ag(111) has been extensively studied and confirmed. However, the nature of the transition stage between the initial Ag2Ge alloy phase at 1/3 monolayer (ML) and the final quasifreestanding phase germanene phase at coverage ≥1 ML still remains elusive. Using angle-resolved photoemission spectroscopy, scanning-tunneling microscopy (STM), and low-energy electron diffraction, we confirm the existence of striped-phase (SP) germanene in the transition stage. Along the armchair direction of SP, the period of higher-order coincidence corresponds to 11aAC=31aAg(111), which accommodates four stripes on the bridge sites of the underlying Ag(111) lattice, as manifested in STM topography. On the electronic-structure side, the splitlike surface band of Ag2Ge centered at the surface zone boundary M¯Ag(111) evidently evolves to a steep, V-shaped interfacial-state band, characteristic of SP germanene. Moreover, an anomalous broad Ag bulk-state band was observed to fully develop upon formation of SP germanene. The bulk-state band originates from the direct transition to the final-state bands of originally d character at ∼22–23eV above the Fermi level. Because of the strong hybridization between germanene and Ag d orbitals, the unoccupied Ag bulk final-state d bands near the interface take on pz character, inducing the direct transition from the Ag bulk occupied pz-valence band, following the selection rule for the photoemission cross section. A germanene identity of SP is thus confirmed. Our result indicates a very important missing segment of the evolution from the initial surface alloy phase to the final Xene layer, which is the coexistence of both in a common stripe lattice during a continuous transition.

Published by the American Physical Society
2024
Stimulated emission tomography for efficient characterization of spatial entanglement
Authors: Xu Yang , Choudhary Saumya , Boyd Robert W. 
Published: November 2024

Stimulated-emission tomography (SET) is an excellent tool for characterizing the process of spontaneous parametric down conversion (SPDC), which is commonly used to create pairs of entangled photons for use in quantum information protocols. The use of stimulated emission increases the average number of detected photons by several orders of magnitude compared to the spontaneous process. In a SET measurement, the parametric down conversion is seeded by an intense signal field prepared with specified mode properties rather than by broadband multimodal vacuum fluctuations, as is the case for the spontaneous process. The SET process generates an intense idler field in a mode that is the complex conjugate to the signal mode. In this work we use SET to estimate the joint spatial mode distribution (JSMD) in the Laguerre-Gaussian (LG) basis of the two photons of an entangled photon pair. The pair is produced by parametric down conversion in a beta barium borate (BBO) crystal with type-II phase matching pumped at a wavelength of 405 nm along with a 780 nm seed signal beam prepared in a variety of LG modes to generate an 842 nm idler beam of which the spatial mode distribution is measured. We observe strong idler production and good agreement with the theoretical prediction of its spatial mode distribution. Our experimental procedure should enable the efficient determination of the photon-pair wavefunctions produced by low-brightness SPDC sources and the characterization of high-dimensional entangled-photon pairs.

Published by the American Physical Society
2024
Beyond replacement and absorption: exploring integrative pathways to accounting colonisation
Authors: Borell Anton 
Published: November 2024

PurposePrior studies have treated colonisation as a process whereby traditional values in public sector settings are replaced by economic ones, driven by the extensive use and visibility of accounting instruments. This paper challenges this conceptualisation by proposing that colonisation can also be integrative, rather than merely a replacing process.Design/methodology/approachThe study employs a qualitative research approach, utilising interviews, observations and documents obtained in a Swedish municipality. The primary focus is on the introduction of economic, market-oriented reforms in a compulsory school setting, a site traditionally guided by welfare values.FindingsThe paper demonstrates that a range of situations has emerged wherein actors attempted to integrate market-oriented and welfare values through various accounting techniques. It also shows how this integration led to colonising outcomes, stemming from an underlying premise of aligning welfare values with a market-like agenda.Originality/valueThis paper contributes to existing research by exploring the complexities and nuances of colonisation and the role of accounting in the interplay between economic and traditional values in public sector settings. It particularly adds to recent studies by outlining a specific form of integrative colonisation, which focusses on a calculative and technical approach to reconciling seemingly disparate values.
Does the proportion of female director influence corporate sustainability disclosure? Evidence from the emerging market firms with two-tier system
Authors: Zulvina Desi , Setiawan Doddy 
Published: November 2024

Purpose
This study aims to explore the influence of critical mass of female directors on corporate sustainability disclosure in emerging market firms with two-tier boards system. Critical mass of female director presented by three types of female director proportion, there are women on board of director (BOD) that are less than 20%, between 20% and 40% and more than 40%.

Design/methodology/approach
The observation comprises 456 firm-year firms listed on the Indonesia Stock Exchange for the period from 2017 to 2022. This study used the static panel data model and dynamic panel data model based on generalize method of moments.

Findings
The research discovered that the proportion of female director has positive effect on corporate sustainability disclosure in emerging market firms with two-tier boards system. The mass of female director with at least 20% but less than 40% has positive relationship on corporate sustainability disclosure. Moreover, the mass of female with balance proportion on BOD has stronger positive impact on corporate sustainability disclosure. However, there is insignificant impact between the mass of female directors and corporate sustainability disclosure with less than 20% proportion of female director.

Practical implications
The companies must facilitate the involvement of women on the board of directors to promote pro-sustainability disclosure initiatives. The findings indicate that corporations should deliberately examine the ratio of female directors to enhance corporate sustainability disclosure.

Originality/value
The research studies will add value to the limited literature and addressed the dynamic nature of the relationship and mitigated the endogeneity bias.