bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diphthamide formation in Arabidopsis requires DPH1-interacting DPH2 for light and oxidative stress resistance
Authors: Zhang Hongliang , Janina Nadežda , Ütkür Koray , Manivannan Thirishika , Zhang Lei , Wang Lizhen , Grefen Christopher , Schaffrath Raffael , Krämer Ute 
Published: September 2024

AbstractDiphthamide is a post-translationally modified histidine residue of eukaryotic TRANSLATION ELONGATION FACTOR 2 (eEF2) and the target of diphtheria toxin in human cells. In yeast and mammals, the 4Fe-4S cluster-containing proteins Dph1 and Dph2 catalyze the first biosynthetic step of diphthamide formation. Here we identifyArabidopsis thalianaDPH2 and show that it is required for diphthamide biosynthesis, localizes to the cytosol and interacts physically with AtDPH1. Arabidopsisdph2mutants form shorter primary roots and smaller rosettes than the wild type, similar todph1mutants which we characterized previously. Additionally, increased ribosomal -1 frameshifting error rates and attenuated TARGET OF RAPAMYCIN (TOR) kinase activity indph2mutants also phenocopy thedph1mutant. Beyond the known heavy-metal hypersensitivity and heat shock tolerance ofdph1, we newly show here that bothdph1anddph2mutants are hypersensitive to elevated light intensities and oxidative stress, and that wild-type Arabidopsis seedlings accumulate diphthamide-unmodified eEF2 under oxidative stress. Both mutants share the deregulation of 1,186 transcripts in numerous environmental and hormone responses. AtDPH1 and AtDPH2 do not complement the corresponding mutants ofSaccharomyces cerevisiae. In summary, DPH2 and DPH1 interact to function inter-dependently in diphthamide formation, the maintenance of translational fidelity, wild-type growth rates and TOR kinase activation, and they contribute to mitigating damage from elevated light intensities and oxidative stress. Under oxidative stress, a dose-dependent loss of diphthamide could potentiate downstream effects in a feed-forward loop. This work advances our understanding of translation and its interactions with growth regulation and stress responses in plants.
Conformational flexibility is a critical factor in designing broad-spectrum human norovirus protease inhibitors
Authors: Pham Son , Zhao Boyang , Neetu Neetu , Sankaran Banumathi , Patil Ketki , Ramani Sasirekha , Song Yongcheng , Estes Mary K. , Palzkill Timothy , Prasad B.V. Venkataram 
Published: September 2024

ABSTRACTHuman norovirus (HuNoV) infection is a global health and economic burden. Currently, there are no licensed HuNoV vaccines or antiviral drugs available. The protease encoded by the HuNoV genome plays a critical role in virus replication by cleaving the polyprotein and is, therefore, an excellent target for developing small molecule inhibitors. While rupintrivir, a potent small-molecule inhibitor of several picornavirus proteases, effectively inhibits GI.1 protease, it is an order of magnitude less effective against GII protease. Other GI.1 protease inhibitors also tend to be less effective against GII proteases. To understand the structural basis for the potency difference, we determined the crystal structures of proteases of GI.1, pandemic GII.4 (Houston and Sydney), and GII.3 in complex with rupintrivir. These structures show that the open substrate pocket in GI protease binds rupintrivir without requiring significant conformational changes, whereas, in GII proteases, the closed pocket flexibly extends, reorienting arginine-112 in the BII-CII loop to accommodate rupintrivir. Structures of R112A protease mutants with rupintrivir, coupled with enzymatic and inhibition studies, suggest R112 is involved in displacing both substrate and ligands from the active site, implying a role in the release of cleaved products during polyprotein processing. Thus, the primary determinant for differential inhibitor potency between the GI and GII proteases is the increased flexibility in the BII-CII loop of the GII proteases caused by H-G mutation in this loop. Therefore, the inherent flexibility of the BII-CII loop in GII proteases is a critical factor to consider when developing broad-spectrum inhibitors for HuNoV proteases.IMPORTANCEHuman noroviruses are a significant cause of sporadic and epidemic gastroenteritis worldwide. There are no vaccines or antiviral drugs currently available to treat infections. Our work elucidates the structural differences between GI.1 and GII proteases in response to inhibitor binding and will inform the future development of broad-spectrum norovirus protease inhibitors.
Exploring putative enteric methanogenesis inhibitors using molecular simulations and a graph neural network
Authors: Aryee Randy , Mohammed Noor S. , Dey Supantha , Arunraj B. , Nadendla Swathi , Sajeevan Karuna Anna , Beck Matthew R. , Frazier A. Nathan , Koziel Jacek A. , Mansell Thomas J. , Chowdhury Ratul 
Published: September 2024

ABSTRACTAtmospheric methane (CH4) acts as a key contributor to global warming. As CH4is a short-lived climate forcer (12 years atmospheric lifespan), its mitigation represents the most promising means to address climate change in the short term. Enteric CH4(the biosynthesized CH4from the rumen of ruminants) represents 5.1% of total global greenhouse gas (GHG) emissions, 23% of emissions from agriculture, and 27.2% of global CH4emissions. Therefore, it is imperative to investigate methanogenesis inhibitors and their underlying modes of action. We hereby elucidate the detailed biophysical and thermodynamic interplay between anti-methanogenic molecules and cofactor F430of methyl coenzyme M reductase and interpret the stoichiometric ratios and binding affinities of sixteen inhibitor molecules. We leverage this as prior in a graph neural network to first functionally cluster these sixteen known inhibitors among ∼54,000 bovine metabolites. We subsequently demonstrate a protocol to identify precursors to and putative inhibitors for methanogenesis, based on Tanimoto chemical similarity and membrane permeability predictions. This work lays the foundation for computational andde novodesign of inhibitor molecules that retain/ reject one or more biochemical properties of known inhibitors discussed in this study.COVER ABSTRACT
Fish environmental RNA sequencing sensitively captures accumulative stress responses through short-term aquarium sampling
Authors: Miyata Kaede , Inoue Yasuaki , Yamane Masayuki , Honda Hiroshi 
Published: September 2024

AbstractThe utility of environmental RNA (eRNA) in capturing biological responses to stresses has been discussed previously; however, the limited number of genes detected remains a significant hindrance to its widespread implementation. Here, we investigated the potential of eRNA to assess the health status of Japanese medaka fish exposed to linear alkylbenzene sulfonate. Analyzing eRNA and organismal RNA (oRNA) in aquarium water for > 12 h, we achieved high mapping rates and 10 times more differentially expressed genes than previously reported. This advancement has facilitated the previously unattainable capability of gene ontology (GO) analysis. In GO analysis, it was found that eRNA could detect nuclear genes in cellular component, and oRNA provided gene expression signatures in the short term, whereas eRNA demonstrated the potential to reflect cumulative gene expression signatures over a period of time in biological process. Moreover, eRNA exhibited high sensitivity in responding to genes associated with sphingolipid and ceramide biosynthesis, which are involved in inflammatory responses possibly originating from impaired cells. This finding aligns with the observations made in oRNA. Conclusively, eRNA-sequencing (eRNA-seq) using aquarium water emerges as a valuable high sensitivity tool for analyzing physiological stress. The findings of this study lay the foundation for further development of eRNA-seq technologies.
A high-resolution microscopy system for biological studies of cold-adapted species under physiological conditions
Authors: Marty Anne-Pia M. , Ward Edward N. , Lamb Jacob R. , van Tartwijk Francesca W. , Peck Lloyd S. , Clark Melody S. , Kaminski Clemens F. 
Published: September 2024

AbstractThe fundamental processes governing life are sensitively dependent on temperature. Whilst much is known about the constraints on how proteins operate at 37°C, little knowledge exists about how biological function is maintained sub-zero temperature conditions, where proteins are less stable and oxidative damage is high. However, almost 90% of habitable environments on Earth are permanently below 5°C (i.e. the deep sea and polar regions). This means that we do not understand how a large and diverse proportion of the global biome functions. To address this question at the cellular level, tools are required for imaging biological systems at high resolution under physiological conditions. This poses severe technical challenges that cannot be addressed with traditional optical microscopy techniques. High-resolution imaging objectives require short working distances and the use of immersion media, which lead to rapid heat transfer from the microscope to the sample. This affects the viability of live specimens and the interpretability of the results when the sample function optimally at low temperatures. Condensation and temperature-induced shrinking of components pose further challenges, reducing image resolution and contrast. Here, we address these issues and provide a method for high-fidelity imaging of live biological samples at temperatures of around, or below, 0°C. Our method is compatible with different microscopy modalities, including super-resolution imaging. It relies on hardware additions to traditional microscopy systems that can be straightforwardly implemented, namely, a cooling collar, 10% ethanol as an immersion medium, and nitrogen flow to mitigate condensation. We demonstrate the method in live cell cultures derived from Antarctic fish species and highlight the need to maintain physiological conditions for these fragile biological samples. Future applications are diverse and include evolutionary biology and the study of cold-adapted organisms, as well as cellular biophysics and several applications in biotechnology.
Expression of XCR1, CX3CR1, CSF1R and ADGRE1 on subsets of bovine blood dendritic cells and monocytes
Authors: Talker Stephanie C , Wu Zhiguang , Dry Inga , Summerfield Artur , Hope Jayne C 
Published: September 2024

AbstractAmong dendritic cells (DC) and monocytes in blood of cattle we can distinguish conventional and plasmacytoid DC (cDC1, cDC2, pDC) and classical, intermediate and nonclassical monocytes (cM, intM, ncM), respectively. Phenotypic definitions of subsets rely on combinations of only a few markers such as CD13 and CD4 for Flt3+dendritic cells, and CD14 and CD16 for CD172ahighmonocytes. Additional reagents for flow cytometry are urgently needed to refine these phenotypic classifications and account for heterogeneity of these cells, in particular cDC2 and intM.In the current study we have investigated expression of CX3CR1 and ADGRE1 on bovine blood DC and monocyte subsets, and have tested two newly generated bovine recombinant proteins (XCL1 and CSF1) for staining of XCR1 and CSF1R.Staining patterns obtained by multicolor flow cytometry of peripheral blood mononuclear cells from two cows were largely in line with gene expression data available from a previous study (bulk RNA-seq of sorted DC and monocyte subsets from bovine blood).
Highly accurate assembly polishing with DeepPolisher
Authors: Mastoras Mira , Asri Mobin , Brambrink Lucas , Hebbar Prajna , Kolesnikov Alexey , Cook Daniel E. , Nattestad Maria , Lucas Julian , Won Taylor S. , Chang Pi-Chuan , Carroll Andrew , Paten Benedict , Shafin Kishwar 
Published: September 2024

AbstractAccurate genome assemblies are essential for biological research, but even the highest quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typically fixed with an additional polishing step that uses reads aligned to the draft assembly to identify necessary edits. However, current methods struggle to find a balance between over- and under-polishing. Here, we present an encoder-only transformer model for assembly polishing called DeepPolisher, which predicts corrections to the underlying sequence using Pacbio HiFi read alignments to a diploid assembly. Our pipeline introduces a method, PHARAOH (Phasing Reads in Areas Of Homozygosity), which uses ultra-long ONT data to ensure alignments are accurately phased and to correctly introduce heterozygous edits in falsely homozygous regions. We demonstrate that the DeepPolisher pipeline can reduce assembly errors by half, with a greater than 70% reduction in indel errors. We have applied our DeepPolisher-based pipeline to 180 assemblies from the next Human Pangenome Reference Consortium (HPRC) data release, producing an average predicted Quality Value (QV) improvement of 3.4 (54% error reduction) for the majority of the genome.
A new highly specific and soluble protease for precise removal of N-terminal purification tags
Authors: Shams Raef , Regan Lynne 
Published: September 2024

AbstractThe affinity purification tags have significantly enhanced the ease of purification of many proteins. After purification, it is necessary to remove the affinity purification tag for many applications. Several specific proteases have been developed for tag removal, but none yet has both, a desirable cleavage specificity and high solubility. Here we describe the design and characterization of a novel protease, which we have named Con1, which exhibits desirable cleavage specificity and high solubility. We present a detailed analysis of the kinetic properties of Con1, along with demonstrating its ability to remove purification tags from different proteins.
Integrating Clinical Research with Electronic Health Records to Improve Diversity in Research: Findings from an Urban Hospital System
Authors: Brown Edward H. , Peiper Nicholas C. , Furmanek Stephen , McCants Kelly 
Published: September 2024

AbstractBackgroundThe under-representation of racial, ethnic, and other minority populations in clinical research has threatened the validity of novel therapeutic interventions and exacerbated the longstanding inequities in health outcomes. Despite attention and mandates across institutions and federal agencies to address these disparities, effective and actionable strategies have remained a subject of debate in the existing literature. Thus, the need for comprehensive and rigorous methods to assess diversity in study population samples as well as strategies for improved recruitment and retention has been made clear.ObjectiveExamine the distribution of research participant demographics at Norton Healthcare (NHC) and compare to applicable benchmarks from the overall NHC patient population and local census.DesignSuccessive-independent samples comparison of EPIC electronic health records (EHR) and census data from Jefferson County.ParticipantsA total of 2,053 adult research participants enrolled at NHC from 2020 – 2024.Main MeasuresDemographic data were reported as frequency and percentage across the three benchmarks. The z-test for independent proportions was used to compare the research participant demographics to the NHC patients and Jefferson County during a consistent time period. Temporal trends in research participant demographics were also examined.Key ResultsApart from being relatively older, the NHC research participant population closely resembled the NHC patient population. A similar age-related pattern emerged as well as an over-representation of White individuals in the research participant group when compared to the census data. When looking at research participant demographic trends overtime, increases in White, Black and older cohorts were noted while decreases were observed in Hispanic/Latinx and younger cohorts. Trends related to participant sex remained stable.ConclusionsThe findings from this study will inform future strategies for setting enrollment goals and facilitate the creation of tools and metrics to evaluate appropriate standards for diversity in clinical research study population samples.
Behavioural rhythms of two gammarid speciesEchinogammarus marinusandGammarus pulexunder increasing levels of light at night
Authors: Underwood Charlotte N. , Ford Alex T. , Robson Samuel C. , Wijnen Herman 
Published: September 2024

AbstractArtificial light at night (ALAN) is proliferating at an alarming rate across the globe, particularly around aquatic habitats. Natural and predictable light cycles dictate much of an individual organism’s life by acting as a major signal for their circadian clock, driving rhythmic behaviours and physiological changes throughout the body. Light cycles also help populations coordinate group behaviour and greatly impact the interspecies dynamics of a community. Research into the ecological impacts of ALAN has highlighted numerous effects on these biological processes, including higher predation rates, impaired growth and development, and diminished reproductive success. Invertebrates play an undeniable role in ecosystem functioning and show robust daily rhythms. As such, it is vital to understand how ALAN may disrupt their behavioural patterns. The aim of this study was to monitor the impacts of increasing levels of light at night (0 lux – 80 lux), as well as constant light and constant darkness, on the behavioural rhythms of the intertidal amphipod,Echinogammarus marinus, and the freshwater species,Gammarus pulex. G. pulexactivity was not strongly synchronised to any of the light at night treatments.E. marinus, however, exhibited strong behavioural rhythmicity in diurnal cycles with dark night periods. All the ALAN treatments resulted in a significant decrease inE. marinusrhythmicity and overall activity. Moreover, ALAN between 1-50 lux disrupted nocturnality in this species. These results indicate that while some gammarids show some adaptive plasticity when it comes to light pollution, others may experience strong direct impacts on their activity. This may be relevant to individual and population level fitness of vulnerable species in more heavily urbanised areas.
Computational Analysis of Human Cysteine Redox Proteoforms Reveals Novel Insights
Authors: Cobley James N. , Chatzinikolaou Panagiotis N. , Schmidt Cameron 
Published: September 2024

AbstractSince cysteine redox proteoforms (i) are virtually unstudied, we derived novel insights by computationally analysing the human proteome. Our analysis revealed a vast, effectively infinite, theoreticalispace housing 3.02 x 10169unique cysteine redox proteoforms. For >80% and 99% of the human proteome, theispace comprises 6.83 x 108and 1.76 x 1031unique proteoforms, respectively. The heterogenous distribution of theispace by gene ontology terms, suggests, but does not prove, functional speciation. To theoretically limit the number of cysteine redox proteoforms that can be “downloaded” from the abstracti“cloud”, we implement novel equations. Protein copy numbers limit theispace by 161-logs to 4.04 x 107unique cysteine redox proteoforms per HeLa cell. An immutable law: the number of cysteine redox proteoform molecules (Ni) must equal the number of cysteine-containing protein molecules. We compute anNivalue of 1.70 x 109per HeLa cell. WhileNiwill be displaced from thermodynamic equilibrium towards the reduced state (e.g., ≈90%-reduced), it is possible that the number of partially oxidised cysteine redox proteoform molecules is in the order of 106-8per HeLa cell. Consistent with this, 100%-oxidised forms were observed in 60% of the proteins studied to date. Our analysis advances understanding of redox biology at the proteoform level.
An Inflammation Centered Perspective to the Mechanisms and Interactions Related to Vascular Cognitive Impairment
Authors: Zeylan Melisa Ece , Senyuz Simge , Keskin Ozlem , Gursoy Attila 
Published: September 2024

ABSTRACTA major health burden for the elderly, vascular cognitive impairment (VCI) is a disease that combines cognitive (CD) and cardiovascular (CVD) components. The molecular mechanisms underlying this disease are poorly understood, and our work attempts to bridge this knowledge gap by building protein-protein interaction (PPI) networks of CD and CVD. Our earlier research not only showed how well these two primary components work together, but also hinted at the potential role of inflammation in the development of VCI. For this reason, we decided to examine the relationship between inflammation and VCI in further detail.We identified the top three most connected clusters, which could represent significant modules, enriched these clusters with alternative conformations, and used PRISM to predict the interactions between the conformations. We proposed putative VCI-related interactions, such as NFKBIA-RELA and the proteasome complex, as well as their effects. The five interactions that we discovered have a higher predicted binding affinity when one of the conformations is mutated: LTF-SNCA, FGA-LTF, UBE2D1-VCP, ERBB4-INS, and NFE2L2-VCP. Additionally, since VCP has a conformational mutation linked to dementia, we proposed that the cancer-related protein BRCA1 may have implications for VCI. BRCA1’s interaction with both wild-type and mutant XRCC4 and LIG4 suggests the significance of the DNA damage response pathway which can be shared between VCI and cancer.Altogether, our results suggest various pathways and interactions that can act as targets for therapeutic interventions or early diagnosis of VCI.
Phosphorylation-induced SUMOylation promotes Ulk4 condensation at ciliary tip to transduce Hedgehog signal
Authors: Zhou Mengmeng , Han Yuhong , Jiang Jin 
Published: September 2024

AbstractHedgehog (Hh) signaling controls embryonic development and adult tissue homeostasis through the Gli family of transcription factors. In vertebrates, Hh signal transduction depends on the primary cilium where Gli is thought to be activated at the ciliary tip, but the underlying mechanism has remained poorly understood. Here we provide evidence that twoUnc-51-likekinase (Ulk) family members Stk36 and Ulk4 regulate Gli2 ciliary tip localization and activation through phosphorylation and SUMOylation-mediated condensation in response to Shh. We find that Stk36-mediated phosphorylation of Ulk4 promotes its SUMOylation in response to Shh, and the subsequent interaction between SUMO and aSUMO-Interacting-Motif (SIM) in the C-terminal region of Ulk4 drives Ulk4 self-assembly to form biomolecular condensates that also recruit Stk36 and Gli2. SUMOylation or SIM-deficient Ulk4 failed to accumulate at ciliary tip to activate Gli2 whereas phospho-mimetic mutation of Ulk4 sufficed to drive Ulk4/Stk36/Gli2 condensation at ciliary tip, leading to constitutive Shh pathway activation in a manner dependent on Ulk4 SUMOylation. Taken together, our results suggest that phosphorylation-dependent SUMOylation of Ulk4 promotes kinase-substrate condensation at ciliary tip to transduce the Hh signal.