bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding Phospho-Regulation and Flanking Regions in Autophagy-Associated Short Linear Motifs: A Case Study of Optineurin-LC3B Interaction
Authors: Antonescu Oana N. , Utichi Mattia , Sora Valentina , Tiberti Matteo , Maiani Emiliano , Lambrughi Matteo , Papaleo Elena 
Published: October 2023

AbstractShort Linear Motifs (SLiMs) play a pivotal role in mediating interactions between intrinsically disordered proteins and their binding partners. SLiMs exhibit sequence degeneracy and undergo regulation through post-translational modifications, including phosphorylation. The flanking regions surrounding the core motifs also exert a crucial role in shaping the modes of interaction. In this study, we aimed to integrate biomolecular simulations, in silico high-throughput mutational scans, and biophysical experiments to elucidate the structural details of phospho-regulation in a class of SLiMs crucial for autophagy, known as LC3 interacting regions (LIRs). As a case study, we investigated the interaction between optineurin and LC3B. Optineurin LIR perfectly exemplify a class of LIR where there is a complex interplay of different phosphorylations and a N-terminal helical flanking region to be disentangled. Our work unveils the unexplored role of the N-terminal flanking region upstream of the LIR core motif in contributing to the interaction interface. The results offer an atom-level perspective on the structural mechanisms and conformational alterations induced by phosphorylation in optineurin and LC3B recognition, along with of effects of mutations on the background of the phosphorylated form of the protein. Additionally, we assessed the impact of disease-related mutations on optineurin, accounting for different functional features.Notably, we established an approach based on Microfluidic Diffusional Sizing as a novel method to investigate the binding affinity of SLiMs to target proteins, enabling precise measurements of the dissociation constant for a selection of variants identified in the in silico mutational screening. Overall, our work provides a versatile toolkit to characterize other LIR-containing proteins and their modulation by phosphorylation or other phospho-regulated SLiMs, thereby advancing the understanding of important cellular processes.
Successive responses of three coral holobiont components (coral hosts, symbiotic algae, and bacteria) to daily temperature fluctuations
Authors: Hsieh Yunli Eric , Lu Chih-Ying , Liu Po-Yu , Kao Jia-Min , Yang Sung-Yin , Wu Chien-Yi , Wong Jing-Wen Michelle , Shikina Shinya , Fan Tung-Yung , Yang Shan-Hua 
Published: October 2023

AbstractCoral reef ecosystems support over a quarter of the world’s marine life and play important ecological and economic roles. However, the increasingly severe weather events associated with ocean warming and climate change are believed to be rapidly altering the functions of coral reefs and their ecosystems. Corals and their associated microbiota form a “holobiont,” which includes symbiotic algae and other associated microbiota dominated by bacteria. These microbiota have a direct relationship with the health of the coral host. Their composition is influenced by various environmental factors, such as increasing sea water temperatures. Previous studies of the effects of temperature changes on coral physiology and associated bacterial communities have been conducted based on stable water temperatures set by mean temperatures, or by slowly increasing/decreasing temperatures. However, the daily temperature fluctuations that corals experience in nature are not stable. Rather, there may be significant differences of up to 6°C in a single day. The current understanding of the effects of large daily temperature fluctuations on coral and associated bacterial community dynamics is limited. Hence, in this study, we conducted a four-week tank experiment using different large daily temperature fluctuations accompanied by continuous warming conditions to investigate the effects on two common reef-building corals,Stylophora pistillataandPocillopora acuta, in Taiwan. During the experiment, the activity of coral host catalase was measured, the photosynthetic ability of symbiotic algae was recorded, and the variation in bacterial communities was analyzed using the V6-V8 region of 16S rDNA. According to the results, different parts of the holobionts of different coral species exhibited varying response rates to the continuous warming conditions and diurnal temperature fluctuations. Additionally, it was found that diurnal temperature fluctuations may mitigate the heat stress on the host and reduce the changes in bacterial response to warming. Furthermore, the holobionts of different coral species may adopt different adaptation and survival strategies in response to diurnal temperature fluctuations and warming. Finally, based on the response of these two coral species under the conditions of diurnal temperature fluctuations and continuous warming,AcinetobacterandRhodobacteraceaewere identified as potential indicator coral-associated bacteria. This is the first study to investigate the tripartite dynamic response of coral, symbiotic algae and bacteria to daily temperature fluctuations.
Multichannel bioelectronic sensing using engineeredEscherichia coli
Authors: Zhang Xu , Ajo-Franklin Caroline 
Published: October 2023

ABSTRACTBy engineering extracellular electron transfer (EET) to be dependent on an analyte, researchers have developed whole cell bioelectronic sensors that sense hazards to human and environmental health1. However, these sensors regulate a single electron transfer pathway as an electrochemical channel, limiting the sensing information to a single analyte. To increase information content, we developed a multichannel bioelectronic sensor through which different chemicals regulate distinct extracellular electron transfer pathways within a singleEscherichia colicell. One channel utilizes the flavin synthesis pathway fromBacillus subtilis2and the other a set of cytochromes constructing the Mtr pathway fromShewanella oneidensis3. We demonstrate an arsenite responsive promoter can control the Mtr pathway through activation of cytochrome CymA expression and a cadmium responsive promoter can control the flavin synthesis pathway4,5. The redox potential of flavin-mediated EET is different from that of CymA-mediated one6. This allowed for development of a redox-potential-dependent algorithm that distinguishes variable input signals of each analyte mediated by two EET pathways in vivo. This approach enables a 2-bit binary signal readout for real-time tracking throughout the entire sensing duration. Our multichannel bioelectronic sensor was able to accurately sense and distinguish different heavy metals in Brays Bayou water samples with a response time comparable to that in clean water. This multichannel bioelectronic sensors allow for simultaneous detection of different chemicals, significantly expanding information transmission and helping to safeguard human and environmental health.
Wolbachiaenhances the survival ofDrosophilainfected with fungal pathogens
Authors: Perlmutter Jessamyn I. , Atadurdyyeva Aylar , Schedl Margaret E. , Unckless Robert L. 
Published: October 2023

AbstractWolbachiabacteria of arthropods are at the forefront of basic and translational research on multipartite host-symbiont-pathogen interactions. These microbes are vertically inherited from mother to offspring via the cytoplasm. They are the most widespread endosymbionts on the planet due to their infamous ability to manipulate the reproduction of their hosts to spread themselves in a population, and to provide a variety of fitness benefits to their hosts. Importantly, some strains ofWolbachiacan inhibit viral pathogenesis within and between arthropod hosts. Mosquitoes carrying thewMelWolbachiastrain ofDrosophila melanogasterhave a greatly reduced capacity to spread viruses like dengue and Zika to humans. Therefore,Wolbachiaare the basis of several global vector control initiatives. While significant research efforts have focused on viruses, relatively little attention has been given toWolbachia-fungal interactions despite the ubiquity of fungal entomopathogens in nature. Here, we demonstrate thatWolbachiaincrease the longevity of theirDrosophila melanogasterhosts when challenged with a spectrum of yeast and filamentous fungal pathogens. We find that this pattern can vary based on host genotype, sex, and fungal species. Further,Wolbachiacorrelates with higher fertility and reduced pathogen titers during initial fungal infection, indicating a significant fitness benefit. This study demonstratesWolbachia’s role in diverse fungal pathogen interactions and determines that the phenotype is broad, but with several variables that influence both the presence and strength of the phenotype. These results enhance our knowledge of the strategiesWolbachiauses that likely contribute to such a high global symbiont prevalence.ImportanceWolbachiabacteria of arthropods are at the forefront of global initiatives to fight arthropod-borne viruses. Despite great success in using the symbiont to fight viruses, little research has focused onWolbachia-fungal interactions. Here, we find thatWolbachiaofDrosophila melanogaster, the same strain widely used in antiviral initiatives, can also increase the longevity of flies systemically infected with a panel of yeast and filamentous fungal pathogens. The symbiont also partially increases host fertility and reduces fungal titers during early infection, indicating a significant fitness benefit. This represents a major step forward inWolbachiaresearch since its pathogen blocking abilities can now be extended to a broad diversity of another major branch of microbial life. This discovery may inform basic research on pathogen blocking and has potential translational applications in areas including biocontrol in agriculture.
Transcriptional coupling of telomeric retrotransposons with the cell cycle
Authors: Liu Mengmeng , Xie Xiao-Jun , Li Xiao , Ren Xingjie , Sun Jasmine , Lin Zhen , Hemba-Waduge Rajitha-Udakara-Sampath , Ji Jun-Yuan 
Published: October 2023

AbstractInstead of employing telomerases to safeguard chromosome ends, dipteran species maintain their telomeres by transposition of telomeric-specific retrotransposons (TRs): inDrosophila, these areHeT-A,TART, andTAHRE. Previous studies have shown how these TRs create tandem repeats at chromosome ends, but the exact mechanism controlling TR transcription has remained unclear. Here we report the identification of multiple subunits of the transcription cofactor Mediator complex and transcriptional factors Scalloped (Sd, the TEAD homolog in flies) and E2F1-Dp as novel regulators of TR transcription and telomere length inDrosophila. Depletion of multiple Mediator subunits, Dp, or Sd increased TR expression and telomere length, while over-expressing E2F1-Dp or knocking down the E2F1 regulator Rbf1 (Retinoblastoma-family protein 1) stimulated TR transcription, with Mediator and Sd affecting TR expression through E2F1-Dp. The CUT&RUN analysis revealed direct binding of CDK8, Dp, and Sd to telomeric repeats. These findings highlight the essential role of the Mediator complex in maintaining telomere homeostasis by regulating TR transcription through E2F1-Dp and Sd, revealing the intricate coupling of TR transcription with the host cell-cycle machinery, thereby ensuring chromosome end protection and genomic stability during cell division.
Phylogenetic Distribution of Prokaryotic Non-Homologous End Joining DNA Repair Systems in Bacteria and Archaea
Authors: Manoj Femila , Kuhlman Thomas E. 
Published: October 2023

ABSTRACTNonhomologous end-joining (NHEJ) is a repair mechanism for double strand breaks (DSBs) of DNA. This mechanism is ubiquitously observed within the eukaryotic domain; however, its presence is not as pervasive among prokaryotes and archaea. Notably, in prokaryotes, it has been discerned that multiple distinct NHEJ pathways have evolved in contrast to the singular NHEJ pathway prevalent in eukaryotes. We performed phylogenetic analysis to gain deeper insights into the distribution of these prokaryotic NHEJ pathways. Concurrently, components of the prokaryotic NHEJ pathways were used to find if any archaea carry the genes required and may be able to carry out NHEJ. The results show that few prokaryotes carry the components required for NHEJ, but multiple pathways may be active in a single species. In the context of Archaea, the analysis revealed that a substantial number of species contain fragments or segments of prokaryotic NHEJ elements. Nevertheless, the presence of all the necessary components for the complete execution of the NHEJ pathway remains relatively rare within the archaeal domain.
Beyond the “resprouter versus non‐resprouter” dichotomy: On the prevalence and evolutionary fingerprint of resprouting in tropical dry forest trees
Authors: de Souza Cléber Rodrigo , de Coelho de Souza Fernanda , Dexter Kyle G. , Maia Vinícius A. , de Aguiar‐Campos Natália , Farrapo Camila L. , Santos Alisson B. M. , Paula Gabriela G. P. , Morel Jean D. , Fagundes Nathalle C. A. , Santos Paola F. , Coelho Polyanne Aparecida , Silva Wilder B. , Santos Rubens M. 
Published: October 2023

AbstractResprouting is a plant persistence strategy in response to disturbance or stressful environmental conditions. Resprouters can dominate in stressful environments such as tropical dry forests (TDFs), but our knowledge of resprouting in TDFs is limited. Here, using a dataset of forest inventories in 16 TDF fragments (covering 15,642 trees and 321 species), we investigated patterns of resprouting in ecosystems subject to substantial seasonal water stress. We focused on two resprouting metrics: the proportion of trees that are multistemmed (resprouting frequency) and the number of stems per tree. In addition, we investigated the relative importance of environmental factors, taxonomic identity, and evolutionary history in resprouting response. Taxa with low to medium resprouting frequencies (17.19%–40.2%) are the most prevalent in TDF, compared to non‐resprouters and high‐frequency resprouters. Overall, resprouting ability appears to be an intrinsic trait that varies in response to environmental conditions but only within a range constrained by taxonomic identity. However, we found no phylogenetic signal above the genus level for any resprouting variables. Thus, the variation in resprouting across TDF lineages likely has been shaped by divergence between closely related taxa and convergence between distantly related ones, reflecting the specific environmental and disturbance factors to which they have been subjected.
Gut microbiome as a biomarker for predicting early recurrence of HBV‐related hepatocellular carcinoma
Authors: Zheng Chongming , Lu Fei , Chen Bo , Yang Jinhuan , Yu Haitao , Wang Daojie , Xie Haonan , Chen Kaiwen , Xie Yitong , Li Jiacheng , Bo Zhiyuan , Wang Yi , Chen Gang , Deng Tuo 
Published: October 2023

AbstractTo investigate the potential of the gut microbiome as a biomarker for predicting the early recurrence of HBV‐related hepatocellular carcinoma (HCC), we enrolled 124 patients diagnosed with HBV‐associated HCC and 82 HBV‐related hepatitis, and 86 healthy volunteers in our study, collecting 292 stool samples for 16S rRNA sequencing and 35 tumor tissue samples for targeted metabolomics. We performed an integrated bioinformatics analysis of gut microbiome and tissue metabolome data to explore the gut microbial–liver metabolite axis associated with the early recurrence of HCC. We constructed a predictive model based on the gut microbiota and validated its efficacy in the temporal validation cohort. Dialister, Veillonella, the Eubacterium coprostanoligenes group, and Lactobacillus genera, as well as the Streptococcus pneumoniae and Bifidobacterium faecale species, were associated with an early recurrence of HCC. We also found that 23 metabolites, including acetic acid, glutamate, and arachidonic acid, were associated with the early recurrence of HCC. A comprehensive analysis of the gut microbiome and tissue metabolome revealed that the entry of gut microbe‐derived acetic acid into the liver to supply energy for tumor growth and proliferation may be a potential mechanism for the recurrence of HCC mediated by gut microbe. We constructed a nomogram to predict early recurrence by combining differential microbial species and clinical indicators, achieving an AUC of 78.0%. Our study suggested that gut microbes may serve as effective biomarkers for predicting early recurrence of HCC, and the gut microbial–tumor metabolite axis may explain the potential mechanism by which gut microbes promote the early recurrence of HCC.
2‐Hydroxyethyl methacrylate (HEMA): A clinical review of contact allergy and allergic contact dermatitis. Part 2. Cross‐ and co‐sensitization, other skin reactions to HEMA, position of HEMA among (meth)acrylates, sensitivity as screening agent, presence of HEMA in commercial products and practical information on patch test procedures
Authors: de Groot Anton C. , Rustemeyer Thomas 
Published: October 2023

AbstractThis is the second part of a literature review of the clinical aspects of contact allergy to and allergic contact dermatitis from 2‐hydroxyethyl methacrylate (HEMA). Topics include cross‐ and co‐sensitization, atypical manifestations of contact allergy, frequency of positive patch tests to HEMA compared with other (meth)acrylates, sensitivity of HEMA as a screening agent, the presence of HEMA in commercial products, and practical information on patch testing procedures. Primary sensitization to methacrylates including HEMA may result in methacrylate and acrylate cross‐sensitization. There is a strong cross‐allergy between HEMA, ethylene glycol dimethacrylate (EGDMA), and hydroxypropyl methacrylate; many reactions to EGDMA are cross‐reactions to primary HEMA sensitization. Rare atypical manifestations of HEMA‐allergy include lichen planus, lymphomatoid papulosis, systemic contact dermatitis, leukoderma after positive patch tests, and systemic side effects such as nausea, diarrhoea, malaise, and palpitations. The occurrence of respiratory disease caused by methacrylates such as asthma is not infrequent. HEMA is the most frequently patch test‐positive methacrylate. It is a good screening agent for allergy to other (meth)acrylates. Patch test sensitization to HEMA 2% pet. is extremely rare. There are (some) indications that HEMA is frequently used in dental products and nail cosmetics.
Two models of mind blanking
Authors: Kaufmann Angelica , Parmigiani Sara , Kawagoe Toshikazu , Zabaroff Elliot , Wells Barnaby 
Published: October 2023

AbstractMind blanking is a mental state in which attention does not bring any perceptual input into conscious awareness. As this state is still largely unexplored, we suggest that a comprehensive understanding of mind blanking can be achieved through a multifaceted approach combining self‐assessment methods, neuroimaging and neuromodulation. In this article, we explain how electroencephalography and transcranial magnetic stimulation could be combined to help determine whether mind blanking is associated with a lack of mental content or a lack of linguistically or conceptually determinable mental content. We also question whether mind blanking occurs spontaneously or intentionally and whether these two forms are instantiated by the same or different neural correlates.
Placental disposition of cannabidiol: An ex vivo perfusion study
Authors: Berman Erez , Erenburg Natalia , Beloosesky Ron , Eyal Sara , Kovo Michal 
Published: October 2023

AbstractObjectiveIn the absence of safety data in humans, the use of cannabidiol (CBD) is not recommended during pregnancy. Yet >50% of pregnancies in women with epilepsy are unintended, making fetal exposure to CBD possible. As a small‐molecule, highly lipid‐soluble drug, CBD is likely to be distributed into the placenta and cross it. To estimate the placental distribution profile of CBD and its potential short‐term placental effects, we conducted an ex vivo perfusion study in human placentas.MethodsPlacentas were obtained from healthy women undergoing cesarean deliveries. Selected cotyledons were cannulated and perfused for 180 min with a CBD‐containing medium (250 ng/mL, .796 μmol·L−1; representative of a low therapeutic concentration; n = 8). CBD concentrations were determined at 180 min in the medium and placental tissue using liquid chromatography–tandem mass spectrometry. A customized gene panel array was used to analyze the expression of selected genes in the perfused placental cotyledons as well as in placentas perfused with 1000 ng/mL CBD (3.18 μmol·L−1; high therapeutic concentration; n = 8) and in those exposed to the vehicle.ResultsCBD was sequestered in the placental tissue, exhibiting significant variability across samples (median = 5342 ng/g tissue, range = 1066–9351 ng/g tissue). CBD concentrations in the fetal compartment were one fifth of those measured in the maternal compartment (median = 59 ng/mL, range = 48–72 ng/mL vs. 280 = ng/mL, range = 159–388 ng/mL, respectively; p < .01). Placental gene expression was not significantly altered by CBD.SignificanceThe placenta acts as a depot compartment for CBD, slowing down its distribution to the fetus. This phenomenon might yield flatter but prolonged fetal CBD levels in vivo. The attenuated transplacental CBD transfer does not imply that its use by pregnant women is safe for the fetus. Only pregnancy registries and neurocognitive assessments would establish the risk of being antenatally exposed to CBD.
Asian Corporate Governance—and the Case of Dual‐Class Shares: CARE Conference | Hong Kong Polytechnic University | June 9, 2014
Authors: Chan K. C. 
Published: October 2023

The case of the Alibaba IPO illustrates the divergence of corporate governance standards between the United States and many other markets, and reopens the debate on the one‐share one‐vote principle. Since corporate governance standards develop in ways that reflect the history and legal and political environments of different countries, we should not expect to see a global convergence of these standards—nor is it generally desirable to transplant policies from one market to another without understanding their historical backgrounds.Nevertheless, the U.S. approach to regulation raises the concern that competition among exchanges will cause issuers to “shop around” and tempt the exchanges to relax their standards in a race to the bottom. While market participants and regulators outside of the U.S. debate whether and how to modify the one‐share, one‐vote rule, they face challenges in coming up with new rules that strike the right balance between effective corporate governance and market development.