bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear actin is a critical regulator ofDrosophilafemale germline stem cell maintenance
Authors: Green Nicole M. , Talbot Danielle , Tootle Tina L. 
Published: August 2024

ABSTRACTNuclear actin has been implicated in regulating cell fate, differentiation, and cellular reprogramming. However, its roles in development and tissue homeostasis remain largely unknown. Here we uncover the role of nuclear actin in regulating stemness usingDrosophilaovarian germline stem cells (GSCs) as a model. We find that the localization and structure of nuclear actin is dynamic in the early germ cells. Nuclear actin recognized by anti-actin C4 is found in both the nucleoplasm and nucleolus of GSCs. The polymeric nucleoplasmic C4 pool is lost after the 2-cell stage, whereas the monomeric nucleolar pool persists to the 8-cell stage, suggesting that polymeric nuclear actin may contribute to stemness. To test this idea, we overexpressed nuclear targeted actin constructs to alter nuclear actin polymerization states in the GSCs and early germ cells. Increasing monomeric nuclear actin, but not polymerizable nuclear actin, causes GSC loss that ultimately results in germline loss. This GSC loss is rescued by simultaneous overexpression of monomeric and polymerizable nuclear actin. Together these data reveal that GSC maintenance requires polymeric nuclear actin. This polymeric nuclear actin likely plays numerous roles in the GSCs, as increasing monomeric nuclear actin disrupts nuclear architecture causing nucleolar hypertrophy, distortion of the nuclear lamina, and heterochromatin reorganization; all factors critical for GSC maintenance and function. These data provide the first evidence that nuclear actin, and in particular, its ability to polymerize, are critical for stem cell function and tissue homeostasisin vivo.
Enhancing Photosynthesis under Salt Stress via Directed Evolution in Cyanobacteria
Authors: Jiang Zhenxiong , Islam Khondokar Nowshin , Wolfe Malory , O’Connell Michael , Williams Dykia , Florance Ashley , Vinyard David J. , Zhang Xiaohui , Brenner Maxwell , Kiss Andor J. , Liu Xianhua , Wang Xin 
Published: August 2024

AbstractA key aspect of enhancing photosynthesis is improving its recycling kinetics, enabling swift resumption of photochemical quenching following environmental disruptions or stress. Salt stress exacerbates high light stress in cyanobacteria and leads to severe yield losses in crop plants. Genetic traits that confer salt tolerance without compromising photosynthetic performance are essential for improving photosynthesis under these conditions. Here we applied accelerated evolution inSynechococcus elongatusPCC 7942 by conditionally suppressing its methyl-directed mismatch repair system to obtain beneficial genetic traits for enhanced photosynthesis under salt stress. Screening over 10,000 mutants, we isolated eight strains with increased biomass or sucrose productivity under salt stress. Genome sequencing revealed an average of 8-20 single nucleotide polymorphisms (SNPs) or indels per genome. Notably, mutations in the photosystem II (PSII) reaction center D1 gene, resulting in the amino acid changes L353F, I358N, and H359N at the carboxyl terminus of the pre-D1 (pD1) protein, improve photosynthesis under salt and combined salt and light stress by potentially accelerating D1 maturation during PSII repair. Phylogenetic analysis of pD1 across cyanobacteria and red algae highlights the broad significance of these adaptive genetic traits, underscoring the importance of leveraging evolutionary insights to improve photosynthesis under stress or fluctuating environments.
A master regulatory loop that activates genes in a temporally coordinated manner in muscle cells of ascidian embryos
Authors: Oda Izumi , Satou Yutaka 
Published: August 2024

SummaryAscidian larval muscle cells present a classic example of autonomous development. A regulatory mechanism for these cells has been extensively investigated, and the regulatory gene circuit has been documented from maternal factors to a muscle specific gene. In the present study, we comprehensively identified genes expressed specifically in ascidian muscle cells, and found that all of them are under control of a positive regulatory loop ofTbx6-r.bandMrf, the core circuit identified previously. We also found that several transcription factors under control of theTbx6-r.b/Mrfregulatory loop resulted in various temporal expression profiles, which are probably important for creating functional muscle cells. These results, together with results of previous studies, provide an exhaustive view of the regulatory system enabling autonomous development of ascidian larval muscle cells. It shows that theTbx6-r.b/Mrfregulatory loop, but not a single gene, serves a “master” regulatory function. This master regulatory loop not only controls spatial gene expression patterns, but also governs temporal expression patterns in ascidian muscle cells.
Ligand Identification in CryoEM and X-ray Maps Using Deep Learning
Authors: Karolczak Jacek , Przybyłowska Anna , Szewczyk Konrad , Taisner Witold , Heumann John M. , Stowell Michael H.B. , Nowicki Michał , Brzezinski Dariusz 
Published: August 2024

AbstractMotivationAccurately identifying ligands plays a crucial role in the process of structure-guided drug design. Based on density maps from X-ray diffraction or cryogenic-sample electron microscopy (cryoEM), scientists verify whether small-molecule ligands bind to active sites of interest. However, the interpretation of density maps is challenging, and cognitive bias can sometimes mislead investigators into modeling fictitious compounds. Ligand identification can be aided by automatic methods, but existing approaches are available only for X-ray diffraction and are based on iterative fitting or feature-engineered machine learning rather than end-to-end deep learning.ResultsHere, we propose to identify ligands using a deep learning approach that treats density maps as 3D point clouds. We show that the proposed model is on par with existing machine learning methods for X-ray crystallography while also being applicable to cryoEM density maps. Our study demonstrates that electron density map fragments can aid the training of models that can later be applied to cryoEM structures but also highlights challenges associated with the standardization of electron microscopy maps and the quality assessment of cryoEM ligands.AvailabilityCode and model weights are available on GitHub athttps://github.com/jkarolczak/ligands-classification. Datasets used for training and testing are hosted at Zenodo: 10.5281/zenodo.10908325. An accompanying ChimeraX bundle is available athttps://github.com/wtaisner/chimerax-ligand-recognizer.Contact:dariusz.brzezinski@cs.put.poznan.plSupplementary informationSupplementary data are available atBioinformaticsonline.
Short- and Long-term Outcomes of children hospitalized with COVID-19 or Influenza: results of the AUTCOV study
Authors: Wagenlechner Christine , Wendt Ralph , Reichardt Berthold , Mildner Michael , Mascherbauer Julia , Aigner Clemens , Auer Johann , Ankersmit Hendrik Jan , Graf Alexandra Christine 
Published: August 2024

AbstractBackgroundRecent literature gives different results on morbidity and mortality after COVID-19 as compared to Influenza hospitalized children and results of large, population based studies are scant. In this population-based study in Austria, we evaluated and compared the short- and long-term outcomes after COVID-19 or Influenza hospitalization and associations with their baseline drug profile.MethodsIndividual data were provided on children ≤ 18 years hospitalized with COVID-19 in the years 2020 and 2021 or Influenza in 2016 – 2021 as well as on age-, sex- and region-matched controls from the Austrian Health Insurance Funds. The primary outcome was time to hospital discharge. Secondary outcomes were in-hospital death, all-cause mortality and readmission to hospital due to any reason. The median follow-up time was 430 days (IQR: 245-552) in the COVID-19 and 1221 days (IQR: 881-1599) in the Influenza group.Results1063 children were hospitalized due to COVID-19 and 2781 children due to Influenza in the study period. Children hospitalized due to COVID-19 or Influenza were more likely to have a larger disease burden as compared to the general population. Influenza hospitalized patients were observed to be generally younger and a larger percentage of polypharmacy than those with COVID-19. No significant difference in the time to hospital discharge was found between cohorts (HR: 1.22 [95%-CI: 0.97-1.55], p=0.093). The risk for readmission was significantly higher for Influenza (HR: 1.23 [95%-CI: 1.03-1.47], p=0.021). In-hospital mortality (0.94% vs. 0.22%, p=0.004) and long-term mortality (p=0.009) was significantly larger in COVID-19 patients. One-year mortality after hospitalization was estimated with 1.13% (CI: 0.49-1.77) in the COVID and 0.32% (CI: 0.11-0.53) in the Influenza group.ConclusionA general picture of COVID-19 being a milder disease compared to Influenza may not be drawn. No significant difference for time to hospital discharge was observed between cohorts but the risk of readmission was significantly larger in the Influenza group. Death rates of COVID-19 hospitalized children seem to be higher, however, the low number of severe events may limit the findings.
Pericytes require physiological oxygen tension to maintain phenotypic fidelity
Authors: McErlain Tamara , McCulla Elizabeth C , Glass Morgan J , Ziemer Lauren E , Branco Cristina M , Murgai Meera 
Published: August 2024

AbstractPericytes function to maintain tissue homeostasis by regulating capillary blood flow and maintaining endothelial barrier function. Pericyte dysfunction is associated with various pathologies and has recently been found to aid cancer progression. Despite having critical functions in health and disease, pericytes remain an understudied population due to a lack of model systems which accurately reflectin vivobiology. In this study we developed a protocol to isolate and culture murine lung, brain, bone, and liver pericytes, that maintains their known phenotypes and functions. We demonstrate that pericytes, being inherently plastic, benefit from controlled oxygen tension culture conditions, aiding their expansionex vivo. Primary pericytes grown in physioxia (10% O2for lung; 5% O2for brain, bone, and liver) also better retain pericyte phenotypes indicated by stable expression of characteristic transcriptional and protein markers. In functional tube formation assays, pericytes were observed to significantly associate with endothelial junctions. Importantly, we identified growth conditions that limit expression of the plasticity factorKlf4to prevent spontaneous phenotypic switchingin vitro. Additionally, we were able to induce pathological pericyte phenotypic switching in response to metastatic stimuli to accurately recapitulatein vivobiology. Here, we present a robust method for studying pericyte biology in both physiology and disease.
Phase Separation-based Antiviral Decoy Particles as Basis for Programmable Broad-spectrum Therapeutics
Authors: Willinger Or , Granik Naor , Goldberg Sarah , Amit Roee 
Published: August 2024

AbstractTo gain access to cells, viruses employ host proteins as receptors. In soluble form, these receptors are used as decoys to inhibit infection. We fused candidate soluble receptors to an RNA-binding protein, and using synthetic long non-coding RNA (slncRNA) cassettes that can undergo phase-separation we scaffolded the receptor fusions to generate antiviral decoy particles. Using confocal microscopy, we screened antiviral protein candidates by observing changes in phase-separation morphology when incubated with viral-mimicking components. We demonstrated that ACE2 decoy particles bind strongly to the coronavirus RBD, facilitating FRET, while sufficiently sialylated decoy particles form agglutinated structures with RNA peripheries in the presence of a sialolectin. Infection assays show ACE2 decoy particles fully inhibit the Delta and Omicron BA.1 coronavirus variants, and LAMP1 and GYPA decoy particles significantly reduce influenza infectionin-cellulo. This work establishes a foundation for broad-spectrum antiviral decoy particles, composed of multiple receptors targeting various viruses.
Y chromosome STR variation reveals traditional occupation based population structure in India
Authors: Sequeira Jaison Jeevan , Chaitra M. , Rai N R Ananya , Sudeepthi M. , Shalini R. , Mustak Mohammed S , Khanna Jagriti , Sharma Shivkant , Chilukuri Rajendra V E , van Driem George , Shrivastava Pankaj 
Published: August 2024

SummaryEarlier models of grouping Indian populations were based on language families, social stratification and geographical location. Such grouping system has often resulted in oversimplification of ancestry inferences. Moreover, we do not find many studies focused on studying the variation within these groups and the role of past demographic events in shaping them. We analysed the Y-chromosome Short Tandem Repeats haplotypes from 8153 males from India and Eurasia to explore the impact of Holocene migration on the Indian gene pool. We used haplotype variation and date estimates to understand the characteristics of each haplogroup with respect to the different grouping models. Our findings show that the Neolithic agricultural expansion has had a strong influence in shaping the male gene pool of the Indian subcontinent. Haplogroups F, L and R1a contribute greatly towards stratifying Indian populations as hunter-gatherer related, farming-related and priestly groups respectively. Although the caste system enforced endogamy, a traditional occupation based admixture existed since the Neolithic times. Dispersal of haplogroup L from the Near East played a major role in the formation of an agriculturist population that formed an intermediary between the primitive tribes and the R1a-rich priestly group. This study shows that the frequency of R1a in the hunter-gatherer tribes (1.5%) is much lower than previously reported based on other models of population clustering.
Evaluation of Iron Oxide Nanoparticles for Lymph Node Detection with Magnetomotive Ultrasound – A Pilot Study in Rats
Authors: Axelsson Ulrika , Bäckström Sania , Mousavi Arefeh , Persson Linda 
Published: August 2024

AbstractIntroductionThe inadequate detection of lymph node metastases by current imaging methods has led to overtreatment in rectal cancer. Magnetomotive ultrasound (MMUS) has the potential of being a more accurate diagnostic imaging method for lymph node metastases. This method is based on the detection of tissue movement that is induced by the vibration of iron oxide nanoparticles, caused by an external alternating magnetic field. This study investigated the suitability of the subcutaneous administration of two iron oxide nanoparticles—Ferrotran®and Magtrace®—and their distribution in lymph nodes, with regard to the possibility of identifying lymph node metastases in rectal cancer by MMUS.MethodsMale Sprague Dawley rats were injected subcutaneously with 10.7 mg Ferrotran®(n=9), 10.5 mg Magtrace®(n=9), or saline (n=3) dorsally at the root of the tail. On euthanization of the rats after 1, 5, and 24 hours, the proximal and distal lymph nodes were harvested and analyzed by histology [hematoxylin/eosin, Perls Prussian Blue (PPB)] and inductively coupled plasma-optical emission spectroscopy. The primary aim was to evaluate the distribution of the iron oxide nanoparticles throughout the lymphatic system; the general health of the rats after subcutaneous administration of these nanoparticles was also monitored.ResultsAt 1 hour after subcutaneous injection, Ferrotran®and Magtrace®accumulated in the proximal lymph nodes. After 24 hours, both particles had spread to distal lymph nodes, but only Ferrotran®reached the mesenteric and mandibular lymph nodes. In addition, Ferrotran®penetrated the lymph nodes more deeply than Magtrace®at 24 hours. No toxicity was observed with either nanoparticle.ConclusionAlthough both compounds disseminated well, Ferrotran®accumulated better and more rapidly in lymph nodes than Magtrace®. Because accumulation and time are important parameters for imaging, our data indicate that Ferrotran®is a potentially more suitable particle for MMUS in clinical use.
Feedback regulation by the RhoA-specific GEF ARHGEF17 regulates actomyosin network disassembly
Authors: Rao Vasundhara , Grädel Benjamin , Hinderling Lucien , Unen Jakobus Van , Pertz Olivier 
Published: August 2024

AbstractWe report that the RhoA-specific guanine nucleotide exchange factor ARHGEF17 localizes at the back of a fibroblast’s contractile lamella and regulates its disassembly. This localization emerges through retrograde ARHGEF17 transport together with actomyosin flow that most likely involves interactions with ATP-actin at F-actin barbed ends. During this process, ARHGEF17 increasingly oligomerizes into clusters that co-localize with myosin filaments, and correlate with their disassembly at lamella’s distal edge. ARHGEF17 loss of function leads to decreased RhoA activity at the lamella back and impairs its disassembly. High RhoA activity is however maintained at the lamella front where phosphorylated myosin light chain is observed. We propose that the low contractile, disassembling actomyosin network at the lamella back generates barbed ends leading to ATP-actin production, and ARHGEF17 binding. This then locally activates RhoA-dependent contractility, ensuring robust lamella disassembly through fracturing rather than re-inforcement. ARHGEF17 exemplifies the spatio-temporal complexity of Rho GTPase signaling and the requirement of feedback mechanism for homeostasis of contractile actomyosin networks.
Anesthetic-like effects of ketamine inC. elegans
Authors: Seppälä Katariina , Reigada Inés , Matilainen Olli , Rantamäki Tomi , Hanski Leena 
Published: August 2024

ABSTRACTTransparency ofC. elegansenables microscopicin vivoimaging of cellular processes, but immobilization is required due to high locomotor activity. Preservative NaN3is commonly used for this, but is associated with oxidative stress and toxicity. Here, anesthetic-like effects of dissociate anesthetic ketamine inC. elegansare presented using video recordings and infrared-based automated activity tracking. Ketamine caused a reversible blockade of locomotion at a similar concentration (20-50 mM) at which NaN3produces paralysis. Moreover, the recovery rate was remarkably high, and short-term ketamine treatment did not show signs of SKN-1 activation, a marker of the stress response.
Spin Space Groups: Full Classification and Applications
Authors: Xiao Zhenyu , Zhao Jianzhou , Li Yanqi , Shindou Ryuichi , Song Zhi-Da 
Published: August 2024

In this work, we exhaust all the spin space symmetries, which fully characterize collinear, noncollinear, and commensurate spiral as well as incommensurate spiral magnetism, etc., and investigate enriched features of electronic bands that respect these symmetries. We achieve this by systematically classifying the so-called spin space groups (SSGs)—joint symmetry groups of spatial and spin operations that leave the magnetic structure unchanged. Generally speaking, they are accurate (approximate) symmetries in systems where spin-orbit coupling (SOC) is negligible (finite but weaker than the energy scale of interest), but we also show that specific SSGs could remain valid even in the presence of strong SOC. In recent years, SSGs have played increasingly pivotal roles in various fields such as altermagnetism, topological electronic states, and topological magnon, etc. However, due to its complexity, a complete SSG classification has not been completed up to now. By representing the SSGs as O(N) representations, we—for the first time—obtain the complete classifications of 1421, 9542, and 56 512 distinct SSGs for collinear (N=1), coplanar (N=2), and noncoplanar (N=3) magnetism, respectively. SSG not only fully characterizes the symmetry of spin degrees of freedom, but also gives rise to exotic electronic states, which, in general, form projective representations of magnetic space groups (MSGs). Surprisingly, electronic bands in SSGs exhibit features never seen in MSGs, such as (i) nonsymmorphic SSG Brillouin zone, where SSG operations behave as a glide or screw when acting on momentum, (ii) effective π flux, where translation operators anticommute with each other and yield duplicate bands, (iii) higher-dimensional representations unexplained by MSGs, and (iv) unconventional spin texture on a Fermi surface, which is completely determined by SSGs, independent of Hamiltonian details. To apply our theory, we identify the SSG for each of the 1595 published magnetic structures in the MAGNDATA database on the Bilbao Crystallographic Server. Material examples exhibiting the novel features (i)–(iv) are discussed with emphasis. We also investigate new types of SSG-protected topological electronic states that are unprecedented in MSGs. In particular, we propose a 3D Z2 topological insulator state with a fourfold degenerate Dirac point on the surface and a new scenario of anomalous Z2 helical states that appear on magnetic domain walls.

Published by the American Physical Society
2024
Impact of reliable news information on consumers' perceptions and information seeking intentions from a food safety risk
Authors: Yang Cheng-Xian , Baker Lauri M. 
Published: August 2024

PurposeThis study aimed to investigate whether information from reliable news sources such as medical experts and government officials, along with governmental and individual risk responses, influences consumers’ perceptions of news and intention to seek more information. Additionally, it aimed to explore the relationships between these perceptions and consumers’ intentions to seek information in a food safety risk event.Design/methodology/approachA survey design methodology was employed. A quasi-experimental approach divided 470 Taiwanese participants into three groups, each exposed to varying online news content about food safety news, designed according to the Internalization-Distribution-Explanation-Action (IDEA) model. This involved different combinations of reliable sources and risk response advice to examine the impact on news comprehension and behaviour intentions.FindingsThe results indicated that consumers perceived the news as highly credible when they read it with reliable news sources or risk response advice. Governmental and individual risk response advice significantly impacted consumers’ understanding of news. In addition, perceptions of news credibility and understanding of news can increase individuals’ information-seeking intentions to protect themselves from food safety risks.Originality/valueThis study introduced novel insights into the application of the source credibility theory (SCT) model within Taiwanese food safety incidents, identifying key factors that motivate consumer information-seeking behaviour. It marks an initial attempt to incorporate the IDEA model-based risk communication content into research design, aligning with existing literature while highlighting the critical role of reliable sources in enhancing news credibility and consumer response.