bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of human XPD helicase activity with Single Molecule Magnetic Tweezers
Authors: Mao Chunfeng , Mills Maria 
Published: February 2023

ABSTRACTXPD helicase is a DNA unwinding enzyme involved in multiple cellular processes. As part of TFIIH, XPD opens a repair bubble in DNA for access by proteins in the nucleotide excision repair pathway. XPD uses the energy from ATP hydrolysis to translocate in the 5’ to 3’ direction on one strand of duplex DNA, displacing the opposite strand in the process. We used magnetic tweezers assays to measure the double-stranded DNA (dsDNA) unwinding and single-stranded DNA (ssDNA) translocation activities of human XPD by itself. In our experimental setup, hXPD exhibits low unwinding processivity of ~14 bp and slow overall unwinding rate of ~0.3 bp/s. Individual unwinding and translocation events were composed of fast and slow runs and pauses. Analysis of these events gave similar mean run sizes and rates for unwinding and translocation, suggesting that unwinding is a reflection of translocation. The analysis also revealed that hXPD spent similar time stalling and unwinding. hXPD translocated on ssDNA at a similar overall rate as that of unwinding, pointing to an active helicase. However, we observed modest effects of DNA sequence on stalling and unwinding initiation position. Considering the slow unwinding rate, high probability of base pair separation at the ssDNA/dsDNA fork, and the observed DNA sequence dependences, we propose that hXPD is most likely a partially active helicase. Our results provide detailed information on the basal activity of hXPD which enhances our mechanistic understanding of hXPD activity.SIGNIFICANCEHuman XPD helicase is a major component of the general transcription factor TFIIH. TFIIH is essential in both transcription and nucleotide excision repair. Mutations in hXPD are associated with cancers and autosomal recessive disorders. Here we directly measured the dsDNA unwinding and ssDNA translocation of human XPD helicase by itself. Our measurements provide detailed information on the basal activity of human XPD, which enhance our mechanistic understanding of the activity of XPD in the cell, provide a basis for better understanding of the clinical phenotypes, and aid in drug design targeting hXPD related diseases.
Differential regulation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) receptor tetramerization by auxiliary subunits
Authors: Certain Noele , Gan Quan , Bennett Joseph , Hsieh Helen , Wollmuth Lonnie P. 
Published: February 2023

AbstractAMPA receptor (AMPAR) auxiliary subunits are specialized, non-transient binding partners of AMPARs that modulate their ion channel gating properties and pharmacology, as well as their biogenesis and trafficking. The most well characterized families of auxiliary subunits are transmembrane AMPAR regulatory proteins (TARPs) and cornichon homologs (CNIHs) and the more recently discovered GSG1-L. These auxiliary subunits can promote or reduce surface expression of AMPARs in neurons, thereby impacting their functional role in membrane signaling. Here, we show that CNIH-2 enhances the tetramerization of wild type and mutant AMPARs, possibly by increasing the overall stability of the tetrameric complex, an effect that is mainly mediated by interactions with the transmembrane domain of the receptor. We also find CNIH-2 and CNIH-3 show receptor subunit-specific actions in this regard with CNIH-2 enhancing both GluA1 and GluA2 tetramerization whereas CNIH-3 only weakly enhances GluA1 tetramerization. These results are consistent with the proposed role of CNIHs as endoplasmic reticulum cargo transporters for AMPARs. In contrast, TARP γ-2, TARP γ-8, and GSG1-L have no or negligible effect on AMPAR tetramerization. On the other hand, TARP γ-2 can enhance receptor tetramerization but only when directly fused with the receptor at a maximal stoichiometry. Notably, surface expression of functional AMPARs was enhanced by CNIH-2 to a greater extent than TARP γ-2 suggesting that this distinction aids in maturation and membrane expression. These experiments define a functional distinction between CNIHs and other auxiliary subunits in the regulation of AMPAR biogenesis.
Systematic comparison of risky choices in humans and monkeys
Authors: Seak Leo Chi U , Ferrari-Toniolo Simone , Jain Ritesh , Nielsen Kirby , Schultz Wolfram 
Published: February 2023

AbstractThe past decades have seen tremendous progress in fundamental studies on economic choice in humans. However, elucidation of the underlying neuronal processes requires invasive neurophysiological studies that are met with difficulties in humans. Monkeys as evolutionary closest relatives offer a solution. The animals display sophisticated and well-controllable behavior that allows to implement key constructs of proven economic choice theories. However, the similarity of economic choice between the two species has never been systematically investigated. We investigated compliance with the independence axiom (IA) of expected utility theory as one of the most demanding choice tests and compared IA violations between humans and monkeys. Using generalized linear modeling and cumulative prospect theory (CPT), we found that humans and monkeys made comparable risky choices, although their subjective values (utilities) differed. These results suggest similar fundamental choice mechanism across these primate species and encourage to study their underlying neurophysiological mechanisms.
Planarian LDB and SSDP proteins scaffold transcriptional complexes for regeneration and patterning
Authors: Medlock-Lanier Taylor , Clay Kendall B. , Roberts-Galbraith Rachel H. 
Published: February 2023

AbstractSequence-specific transcription factors often function as components of large regulatory complexes. LIM-domain binding protein (LDB) and single-stranded DNA-binding protein (SSDP) function as core scaffolds of transcriptional complexes in animals and plants. Little is known about potential partners and functions for LDB/SSDP complexes in the context of tissue regeneration. In this work, we find that planarian LDB1 and SSDP2 promote tissue regeneration, with a particular function in mediolateral polarity reestablishment. We find that LDB1 and SSDP2 interact with one another and with characterized planarian LIM-HD proteins Arrowhead, Islet1, and Lhx1/5-1.SSDP2andLDB1also function withislet1in polarity reestablishment and withlhx1/5-1in serotonergic neuron maturation. Finally, we show new roles for LDB1 and SSDP2 in regulating gene expression in the planarian intestine and parenchyma; these functions may be LIM-HD-independent. Together, our work provides insight into LDB/SSDP complexes in a highly regenerative organism. Further, our work provides a strong starting point for identifying and characterizing potential binding partners of LDB1 and SSDP2 and for exploring roles for these proteins in diverse aspects of planarian physiology.
Performance of a winter wheat composite cross population in two temperate agroforestry systems – a case study
Authors: Vaccaro Christina , Mascher Fabio , Six Johan , Schöb Christian 
Published: February 2023

AbstractIn agroforestry systems (AFS), where environmental conditions are highly variable at small spatial scales, the use of uniform genetic material of a single cultivar commonly grown in monoculture cropping might not be optimal. However, the use of composite cross populations (CCPs) that contain an inherent genetic variability might be a promising approach to match the environmental variability created by trees in AFS. In this experimental trial, the performance of a CCP (‘CC-2k’) of winter wheat was compared to a commercial variety (‘Wiwa’) in a split-plot design in two AFS (Feusisberg, Wollerau) in Central Switzerland. The factor variety (p < 0.05) and the interactions of site and distance to tree (p < 0.05) and site and variety (p < 0.05) significantly affected wheat yield at the plot level. CC-2k and Wiwa yield (across all distances) amounted to 1.9 ± 0.7 Mg ha−1and 2.0 ± 0.8 Mg ha−1, respectively, in Feusisberg and to 1.9 ± 0.9 Mg ha−1and 0.7 ± 0.4 Mg ha−1, respectively, in Wollerau. Wiwa had a higher protein, Fe and Ca content than CC-2k. Therefore, while the CC-2k outperformed the commercial organic variety Wiwa in terms of yield in one of the two AFS, Wiwa outperformed CC-2k in terms of quality. The composite cross population might be better adapted to the heterogenous environment of agroforestry systems but fails to reach the high-quality product of modern elite cultivars. Further improvements in terms of quality might make CCPs highly interesting for diversified agricultural systems with larger environmental heterogeneity than common monoculture cropping systems.
Three-dimensional fruit growth analysis clarifies developmental mechanisms underlying complex shape diversity in persimmon fruit
Authors: Kusumi Akane , Nishiyama Soichiro , Tao Ryutaro 
Published: February 2023

AbstractHow fruit size and shape are determined is of research interest in agriculture and developmental biology. Fruit typically exhibits three-dimensional structures with genotype-dependent geometric features. Although minor developmental variations have been recognized, little research has fully visualized and measured these variations throughout fruit growth. In this study, a high-resolution 3D scanner was used to investigate the fruit development of 51 persimmon (Diospyros kaki) cultivars with various complex shapes. We obtained 2,380 3D fruit models that fully represented fruit appearance, and enabled precise and automated measurements of unique geometric features throughout fruit development. The 3D fruit model analysis identified key stages that determined the shape attributes at maturity. Typically, genetic diversity in vertical groove development was found, and such grooves can be filled by tissue expansion in the carpal fusion zone during fruit development. Furthermore, transcriptome analysis of fruit tissues from groove/non-groove tissues revealed gene co-expression networks that were highly associated with groove depth variation. The presence ofYABBYhomologs was most closely associated with groove depth and indicated the possibility that this pathway is a key molecular contributor to vertical groove depth variation. These results demonstrate the validity of fruit 3D growth analysis, which is a powerful tool for identifying the developmental mechanisms of fruit shape variation and the molecular basis of this diversity.
Transmissibility of clinically relevant atovaquone-resistantPlasmodium falciparumby anopheline mosquitoes
Authors: Balta Victoria A. , Stiffler Deborah , Sayeed Abeer , Tripathi Abhai K. , Elahi Rubayet , Mlambo Godfree , Bakshi Rahul P. , Dziedzic Amanda G. , Jedlicka Anne E. , Nenortas Elizabeth , Romero-Rodriguez Keyla , Canonizado Matthew A. , Mann Alexis , Owen Andrew , Sullivan David J. , Prigge Sean T. , Sinnis Photini , Shapiro Theresa A. 
Published: February 2023

AbstractRising numbers of malaria cases and deaths underscore the need for new interventions. Long-acting injectable medications, such as those now in use for HIV prophylaxis, offer the prospect of a malaria “chemical vaccine”, combining the efficacy of a drug (like atovaquone) with the durability of a biological vaccine. Of concern, however, is the possible selection and transmission of drug-resistant parasites. We addressed this question by generating clinically relevant, highly atovaquone-resistant,Plasmodium falciparummutants competent to infect mosquitoes. Isogenic paired strains, that differ only by a single Y268S mutation in cytochrome b, were evaluated in parallel in southeast Asian (Anopheles stephensi) or African (Anopheles gambiae) mosquitoes, and thence in humanized mice. Fitness costs of the mutation were evident along the lifecycle, in asexual parasite growth in vitro and in a progressive loss of parasites in the mosquito. In numerous independent experiments, microscopic exam of salivary glands from hundreds of mosquitoes failed to detect even one Y268S sporozoite, a defect not rescued by coinfection with wild type parasites. Furthermore, despite uniformly successful transmission of wild type parasites fromAn. stephensito FRG NOD huHep mice bearing human hepatocytes and erythrocytes, multiple attempts with Y268S-fed mosquitoes failed: there was no evidence of parasites in mouse tissues by microscopy, in vitro culture, or PCR. These studies confirm a severe-to-lethal fitness cost of clinically relevant atovaquone-resistantP. falciparumin the mosquito, and they significantly lessen the likelihood of their transmission in the field.SignificanceNew tools are needed to protect individuals from malaria and to control malaria in the field. Atovaquone plus proguanil is a commonly used and well-tolerated medicine to prevent malaria. No drug resistance has been reported from its prophylactic use, but tablets must be taken daily. Giving atovaquone as a single injection may provide much longer-lasting protection, against both falciparum and vivax malaria, but there is concern this may create drug resistance. In this study we showed that clinically relevant atovaquone-resistant malaria parasites survive poorly, if at all, in mosquitoes, and that mosquitoes do not transmit drug-resistant parasites to humanized mice. These findings lessen the likelihood that an atovaquone “chemical vaccine” would lead to the spread of atovaquone resistance.
Anthelmintic efficacy ofHolarrhena pubescensagainstRaillietinaspp. of domestic fowl through ultrastructural, histochemical, biochemical and GLCM analysis
Authors: Saha Rachita , Gupta Manjil , Majumdar Rima , Saha Subrata , Kar Pradip Kumar 
Published: February 2023

AbstractHolarrhena pubescensis a well-known medicinal plant used in ethno-traditional medicine and tribal folklore medicine in West Bengal, India. This article focuses on depicting the anthelmintic efficacy of ethanolic extract and Ethyl acetate fraction of the stem bark ofHolarrhena pubescensagainst the cestodeRaillietinaspp. through efficacy testing, ultra-structural observations, histochemical and biochemical studies on some tegumental enzymes i.e., Acid Phosphatase (AcPase), Alkaline Phosphatase (AlkPase), Adenosine Triphosphatase (ATPase) and 5’-Nucleotidase (5’-Nu) along with Gray Level Co-occurrence Matrix (GLCM) analysis of histochemistry images. Praziquantel was used as the reference drug. Investigations revealed 10mg/ml of crude extract was determined as the most efficacious dose and the Ethyl acetate fraction showed the most anthelmintic property. Ultrastructural studies through Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM) clearly showed the damage in head, sucker, proglottids, proximal and distal cytoplasm (DC), microtriches (MT), basal lamina (BL), nuclear membrane (NM), and, nucleolus (NL) in the treated worms. Histochemical studies revealed decrease in staining intensity for all the tegumental enzymes in the treated worms compared to control. The GLCM analysis strongly supported the result of histochemical studies. Biochemical studies revealed marked reduction in enzyme activity in the treated worms with maximum reduction in the activity of 5’-Nu (77.8%) followed by ATPase (63.17%).
Benchmarking of novel green fluorescent proteins for the quantification of protein oligomerization in living cells
Authors: Petrich Annett , Aji Amit Koikkarah , Dunsing Valentin , Chiantia Salvatore 
Published: February 2023

AbstractProtein-protein-interactions play an important role in several cellular functions. Quantitative non-invasive techniques are applied in living cells to evaluate such interactions, thereby providing a broader understanding of complex biological processes. Fluorescence fluctuation spectroscopy describes a group of quantitative microscopy approaches for the characterization of molecular interactions at single cell resolution. Through the obtained molecular brightness, it is possible to determine the oligomeric state of proteins. This is usually achieved by fusing fluorescent proteins (FPs) to the protein of interest. Recently, the number of novel green FPs has increased, with consequent improvements to the quality of fluctuation-based measurements. The photophysical behavior of FPs is influenced by multiple factors (including photobleaching, protonation-induced “blinking” and long-lived dark states). Assessing these factors is critical for selecting the appropriate fluorescent tag for live cell imaging applications. In this work, we focus on novel green FPs that are extensively used in live cell imaging. A systematic performance comparison of several green FPs in living cells under different pH conditions using Number & Brightness (N&B) analysis and scanning fluorescence correlation spectroscopy was performed. Our results show that the new FP Gamillus exhibits higher brightness at the cost of lower photostability and fluorescence probability (pf), especially at lower pH. mGreenLantern, on the other hand, thanks to a very highpf, is best suited for multimerization quantification at neutral pH. At lower pH, mEGFP remains apparently the best choice for multimerization investigation. These guidelines provide the information needed to plan quantitative fluorescence microscopy involving these FPs, both for general imaging or for Protein-protein-interactions quantification via fluorescence fluctuation-based methods.
Dynamic mapping of proteome trafficking within and between living cells by TransitID
Authors: Xu Wei Qin , Cheah Joleen S. , Xu Charles , Messing James , Freibaum Brian D. , Boeynaems Steven , Taylor J. Paul , Udeshi Namrata D. , Carr Steven A. , Ting Alice Y. 
Published: February 2023

SummaryThe ability to map trafficking for thousands of endogenous proteins at once in living cells would reveal biology currently invisible to both microscopy and mass spectrometry. Here we report TransitID, a method for unbiased mapping of endogenous proteome trafficking with nanometer spatial resolution in living cells. Two proximity labeling (PL) enzymes, TurboID and APEX, are targeted to source and destination compartments, and PL with each enzyme is performed in tandem via sequential addition of their small-molecule substrates. Mass spectrometry identifies the proteins tagged by both enzymes. Using TransitID, we mapped proteome trafficking between cytosol and mitochondria, cytosol and nucleus, and nucleolus and stress granules, uncovering a role for stress granules in protecting the transcription factor JUN from oxidative stress. TransitID also identifies proteins that signal intercellularly between macrophages and cancer cells. TransitID introduces a powerful approach for distinguishing protein populations based on compartment or cell type of origin.
A Phase 2, Randomized, Double-blind, Placebo-controlled Study of oral RP7214, a DHODH inhibitor, in Patients with Symptomatic Mild SARS-CoV-2 Infection
Authors: Nair Ajit , Barde Prajak , Routhu Kasi V , Vakkalanka Swaroop ,   RP7214-2101 Study Group
Published: February 2023

AbstractIntroductionCOVID-19 pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of immense global public health concern. RP7214, a novel, potent, oral, inhibitor of DHODH, has shown preclinical evidence in inhibiting viral replication and lung inflammation.MethodsThis was a randomized, double-blind, placebo-controlled phase 2 study in patients with symptomatic mild SARS-CoV-2 infection, having at least one high-risk feature (e.g., hypertension, diabetes mellitus) for developing severe Covid-19 infection. The patients received RP7214 (400 mg BID) or a placebo for 14 days in a blinded fashion and were followed up to 30 days. Patients also received supportive therapy (e.g., antipyretics and antitussives for symptomatic relief) at the discretion of the investigator. The endpoints were Covid 19 related hospitalization rate by Day 15, SARS-CoV-2 viral load and clearance on Days 3,7 and 15, clinical symptoms improvement by Day 15, safety, and the immuno-modulatory effect of RP7214.ResultsA total of 163 patients were treated in the study; 82 received RP7214 and 81 received placebo. Of the total patients, 44.2% had received Covid-19 vaccine prior to the study. The symptom onset was ≤ 3 days in 22.1%. None of the patients in the study required hospitalization. There was no difference in the mean change of viral load between RP7214 and placebo. In the subgroup analysis, in patients having symptom onset of ≤ 3 days, RP7214 significantly reduced viral load on Days 3 and 7, respectively. Similarly, in non-vaccinated patients with symptom onset of ≤ 3 days, RP7214 significantly reduced viral load on Day 3. Overall, there was a trend towards better viral load reduction in RP7214-treated patients with a baseline viral load of 5 log units or higher. For all other endpoints, there was no difference between RP7214 and placebo. Majority of the reported AEs were mild and not related either to study treatment.ConclusionsRP7214 at 400 mg BID dose level showed a statistically significant reduction in viral load at an early stage of the disease and in non-vaccinated patients. There was a trend towards better viral load reduction in RP7214-treated patients with a baseline viral load of 5 log units or higher. RP7214 showed a favorable safety profile. Further development of RP7214 in Covid 19 in a mild symptomatic population with co-morbidities and treated at an early stage of disease may show benefit.
Cerebral Topographies of Perceived and Felt Emotions
Authors: Saarimäki H , Nummenmaa L , Volynets S , Santavirta S , Aksiuto A , Sams M , Jääskeläinen IP , Lahnakoski JM 
Published: February 2023

AbstractEmotions modulate behavioral priorities based on exteroceptive and interoceptive inputs, and the related central and peripheral changes may often be experienced subjectively. Yet, it remains unresolved whether the perceptual and subjectively felt components of the emotion processes rely on shared brain mechanisms. We applied functional magnetic resonance imaging, a rich set of emotional movies, and high-dimensional, continuous ratings of perceived and felt emotions depicted in the same movies to investigate their cerebral organization. Eight main dimensions of emotions evoked during natural movie scene perception were represented in the brain across numerous spatial scales and patterns. Perceived and felt emotions generalized both between individuals and between different samples of stimuli depicting the same emotions. The neural affective space demonstrated an anatomical gradient from responses independent of specific emotions in polysensory areas and default mode regions to more localized and emotion-specific discrete processing in subcortical regions. Differences in neural activations during felt and perceived emotions suggest that temporoparietal areas and precuneus have a key role in computing the affective value of the sensory input. This affective value is then transformed into the subjective emotional experience in the anterior prefrontal cortices, cerebellum, and thalamus. Altogether these data reveal the similarities and differences of domain-general and emotion-specific affect networks in the brain during a wide range of perceived and felt emotions.