bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural characterization of a MAPR-related archaeal cytochrome b5M protein
Authors: Teakel Sarah , Marama Michealla , Aragão David , Tsimbalyuk Sofiya , Forwood Jade K. , Cahill Michael A. 
Published: December 2021

AbstractWe recently reported that the membrane associated progesterone receptor (MAPR) protein family (mammalian members: PGRMC1, PGRMC2, NEUFC and NENF) originated from a new class of prokaryotic cytochrome b5 (cytb5) domain proteins, called cytb5M (MAPR-like). Relative to classical cytb5 proteins, MAPR and ctyb5M proteins shared unique sequence elements and a distinct heme binding orientation at an approximately 90⁰ rotation relative to classical cytb5, as demonstrated in the archetypal crystal structure of a cytb5M protein (PDB accession number 6NZX). Here, we present the second crystal structure of an archaeal cytb5M domain (Methanococcoides burtonii WP_011499504.1, PDB:6VZ6). It exhibits similar heme-binding to the 6NZX cytb5M, supporting the deduction that MAPR-like heme orientation was inherited from the prokaryotic ancestor of the original eukaryotic MAPR gene.
Modelling temporal dynamics of genetic diversity in stage-structured plant populations with reference to demographic genetic structure
Authors: Tsuzuki Yoichi , Takada Takenori , Ohara Masashi 
Published: December 2021

AbstractPredicting temporal dynamics of genetic diversity is important for assessing long-term population persistence. In stage-structured populations, especially in perennial plant species, genetic diversity is often compared among life history stages, such as seedlings, juveniles, and flowerings, using neutral genetic markers. Because individuals in mature stages will die and be replaced by those in more immature stages over the course of time, the comparison among stages (sometimes referred to as demographic genetic structure) has been regarded as a proxy of potential genetic changes that accompany the turnover of constituent individuals. However, because demographic genetic structure had not been theoretically examined, the basic property and the validity of demographic genetic structure remained unclear.We developed a matrix model which was made up of difference equations of expected heterozygosity, a common proxy of genetic diversity, of each life history stage at a neutral locus in stage-structured plant populations. Based on the model, we formulated demographic genetic structure as well as the annual change rate of expected heterozygosity (denoted as η). We obtained theoretical expectation of demographic genetic structure and η from our model and compared them with computational results of stochastic simulation for randomly generated 3,000 life histories for model validation. We then examined the relationships of demographic genetic structure with effective population size Ne, which is the determinants of diversity loss per generation time, as well as with η.Theoretical expectations on η and demographic genetic structure fitted well to the results of stochastic simulation, supporting the validity of our model. Demographic genetic structure varied independently of Ne and η, while having a strong correlation with stable stage distribution: expected heterozygosity was lower in stages with fewer individuals.Our results indicate that demographic genetic structure strongly reflects stable stage distribution, rather than temporal genetic dynamics, and that inferring future genetic diversity solely from demographic genetic structure would be misleading. Instead of demographic genetic structure, the newly-defined statistics η will be an useful tool to predict genetic diversity at the same time scale as population dynamics, facilitating evaluation on population viability from a genetic point of view.
A bistable orthogonal prokaryotic differentiation system underlying development of conjugative transfer competence
Authors: Sulser Sandra , Vucicevic Andrea , Bellini Veronica , Moritz Roxane , Delavat François , Sentchilo Vladimir , Carraro Nicolas , van der Meer Jan Roelof 
Published: December 2021

AbstractThe mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that stands model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. The ICE only transfers from a small fraction of cells in a population, which we uncover here, results from a dedicated transfer competence program imposed by the ICE. Transfer competence is orthogonally maintained in individual cells in which it is activated, making them the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.
The Effect of Oblique Image Acquisition on the Accuracy of Quantitative Susceptibility Mapping and a Robust Tilt Correction Method
Authors: Kiersnowski Oliver C. , Karsa Anita , Wastling Stephen J. , Thornton John S. , Shmueli Karin 
Published: December 2021

AbstractPurposeQuantitative susceptibility mapping (QSM) is increasingly used for clinical research where oblique image acquisition is commonplace but its effects on QSM accuracy are not well understood.Theory and MethodsThe QSM processing pipeline involves defining the unit magnetic dipole kernel, which requires knowledge of the direction of the main magnetic field with respect to the acquired image volume axes. The direction of is dependent upon the axis and angle of rotation in oblique acquisition. Using both a numerical brain phantom and in-vivo acquisitions in five healthy volunteers, we analysed the effects of oblique acquisition on magnetic susceptibility maps. We compared three tilt correction schemes at each step in the QSM pipeline: phase unwrapping, background field removal and susceptibility calculation, using the root-mean-squared error and QSM-tuned structural similarity index (XSIM).ResultsRotation of wrapped phase images gave severe artefacts. Background field removal with PDF gave the most accurate susceptibilities when the field map was first rotated into alignment with . LBV and V-SHARP background field removal methods gave accurate results without tilt correction. For susceptibility calculation, thresholded k-space division, iterative Tikhonov regularisation and weighted linear total variation regularisation all performed most accurately when local field maps were rotated into alignment with before susceptibility calculation.ConclusionFor accurate QSM, oblique acquisition must be taken into account. Rotation of images into alignment with should be carried out after phase unwrapping and before background field removal. We provide open-source tilt-correction code to incorporate easily into existing pipelines: https://github.com/o-snow/QSM_TiltCorrection.git.
Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation
Authors: Guilbaud Guillaume , Murat Pierre , Wilkes Helen S. , Lerner Leticia Koch , Sale Julian E. , Krude Torsten 
Published: December 2021

AbstractReplication of the human genome initiates within broad zones of ~ 150 kb. The extent to which firing of individual DNA replication origins within initiation zones is spatially stochastic or localised at defined sites remains a matter of debate. A thorough characterisation of the dynamic activation of origins within initiation zones is hampered by the lack of a high-resolution map of both their position and efficiency. To address this shortcoming, we describe a modification of initiation site sequencing (ini-seq) based on density substitution. Newly-replicated DNA is rendered ‘heavy-light’ (HL) by incorporation of BrdUTP, unreplicated DNA remaining ‘light-light’ (LL). Replicated HL-DNA is separated from unreplicated LL-DNA by equilibrium density gradient centrifugation, then both fractions are subjected to massive parallel sequencing. This allows precise mapping of 23,905 replication origins simultaneously with an assignment of a replication initiation efficiency score to each. We show that origin firing within initiation zones is not randomly distributed. Rather, origins are arranged hierarchically with a set of very highly efficient origins marking zone boundaries. We propose that these origins explain much of the early firing activity arising within initiation zones, helping to unify the concept of replication initiation zones with the identification of discrete replication origin sites.
Discovering tumor-reactive T-cell receptors through single-cell sequencing of tumor-infiltrating lymphocytes
Authors: Gottschalk Elinor , Aksoy Bulent Arman , Aksoy Pinar , Swiderska-syn Marzena , Mart Caroline , Macpherson Linda , Romeo Martin , Smith Aubrey , Knochelmann Hannah , Paulos Chrystal , Timmers Cynthia , Wrangle John , Rubinstein Mark P. , Hammerbacher Jeff 
Published: December 2021

AbstractWe evaluated the utility of single-cell sequencing of tumor-infiltrating lymphocytes (TIL) for tumor-reactive T-cell receptor (TCR) discovery. Using the MC38 cell line as our tumor model in mice, we show that expression of exogenous TCRs via mRNA electroporation in human T cells provides an easy and quick path to validating tumor-specific candidate TCRs. We detail the identification and validation of four novel MC38-reactive mouse TCRs with varying levels of reactivity to the target cells. Validating our process, one of the MC38 TCRs is specific against a previously reported neoantigen (ASMTNMELM in the Adpgk gene). Consideration of these methodologies may aid in the development of rapid TCR-based therapies for the treatment of cancer and human disease.Abstract Figure
Protein proximity networks and functional evaluation of the Casein Kinase 1 γ family reveals unique roles for CK1γ3 in WNT signaling
Authors: Agajanian Megan J. , Potjewyd Frances M. , Bowman Brittany M. , Solomon Smaranda , LaPak Kyle M. , Bhatt Dhaval P. , Smith Jeffrey L. , Goldfarb Dennis , Axtman Alison D. , Major Michael B. 
Published: December 2021

AbstractThe WNT/β-catenin signaling pathway is evolutionarily conserved and controls normal embryonic development, adult tissue homeostasis and regeneration. Aberrant activation or suppression of WNT signaling contributes to cancer initiation and progression, developmental disorders, neurodegeneration, and bone disease. Despite great need and more than 40 years of research, targeted therapies for the WNT pathway have yet to be fully realized. Kinases are exceptionally druggable and occupy key nodes within the WNT signaling network, but several pathway-relevant kinases remain understudied and ‘dark’. Here we studied the function of the CSNK1γ subfamily of human kinases. miniTurbo-based proximity biotinylation and mass spectrometry analysis of CSNK1γ1, CSNK1γ2, and CSNK1γ3 revealed numerous established components of the β-catenin- dependent and independent WNT signaling pathway, as well as novel interactors. In gain-of- function experiments leveraging a panel of transcriptional reporters, CSNK1γ3 but not CSNK1γ1 or CSNK1γ2 activated β-catenin-dependent WNT signaling and the Notch pathway. Within the family, CSNK1γ3 expression uniquely induced LRP6 phosphorylation. Conversely, siRNA- mediated silencing of CSNK1γ3 alone had no impact on WNT signaling, though co-silencing of all three family members decreased WNT pathway activity. We characterized two moderately selective and potent small molecule inhibitors of the CSNK1γ family. These inhibitors and a CSNK1γ3 kinase dead mutant suppressed but did not eliminate WNT-driven LRP6 phosphorylation and β-catenin stabilization. Our data suggest that while CSNK1γ3 expression uniquely drives pathway activity, potential functional redundancy within the family necessitates loss of all three family members to suppress the WNT signaling pathway.
15N metabolic labeling quantification workflow in Arabidopsis using Protein Prospector
Authors: Shrestha Ruben , Reyes Andres V. , Baker Peter R. , Wang Zhi-Yong , Chalkley Robert J. , Xu Shou-Ling 
Published: December 2021

AbstractMetabolic labeling using stable isotopes is widely used for the relative quantification of proteins in proteomic studies. In plants, metabolic labeling using 15N has great potential, but the associated complexity of data analysis has limited its usage. Here, we present the 15N stable-isotope labeled protein quantification workflow utilizing open-access web-based software Protein Prospector. Further, we discuss several important features of 15N labeling required to make reliable and precise protein quantification. These features include ratio adjustment based on labeling efficiency, median and interquartile range for protein ratios, isotope cluster pattern matching to flag incorrect monoisotopic peak assignment, and caching of quantification results for fast retrieval.
The efficacy of antiseptic agents against staphylococcal biofilm can be quantitatively assessed with the use of processed microscopic images
Authors: Krasowski Grzegorz , Migdał Paweł , Woroszyło Marta , Fijałkowski Karol , Chodaczek Grzegorz , Czajkowska Joanna , Dudek Bartłomiej , Nowicka Joanna , Oleksy-Wawrzyniak Monika , Kwiek Bartłomiej , Paleczny Justyna , Brożyna Malwina , Junka Adam 
Published: December 2021

AbstractThe staphylococcal biofilms are major causative factors of non-healing wound infections. Their treatment algorithms recommend the use of locally applied antiseptic agents to counteract the spread of infection. The efficacy of antiseptics against biofilm is assessed in vitro by a set of standard quantitative and semi-quantitative methods. The development of software for image processing allowed to obtain quantitative data also from microscopic images of biofilm dyed with propidium iodine and SYTO-9 reagents, differentiating dead cells from the live ones. In this work, the method of assessment of the impact of antiseptic agents on staphylococcal biofilm in vitro, based on biofilm’s processed images, was proposed and scrutinized with regard to clinically-relevant antiseptics. Taking into account the fact that in vitro results of the efficacy of antiseptic agents against staphylococcal biofilm are frequently applied to back up their use in hospitals and ambulatory units, our work should be considered an important tool providing reliable, quantitative data with this regard.
Elucidating the acid-base mechanisms underlying otolith overgrowth in fish exposed to ocean acidification
Authors: Kwan Garfield T. , Tresguerres Martin 
Published: December 2021

AbstractOver a decade ago, ocean acidification (OA) exposure was reported to induce otolith overgrowth in teleost fish. This phenomenon was subsequently confirmed in multiple species; however, the underlying physiological causes remain unknown. Here, we report that splitnose rockfish (Sebastes diploproa) exposed to ~1,600 μatm pCO2 (pH ~7.5) were able to fully regulated the pH of both blood and endolymph (the fluid that surrounds the otolith within the inner ear). However, while blood was regulated around pH 7.80, the endolymph was regulated around pH ~8.30. These different pH setpoints result in increased pCO2 diffusion into the endolymph, which in turn leads to proportional increases in endolymph [HCO3−] and [CO32−]. Endolymph pH regulation despite the increased pCO2 suggests enhanced H+ removal. However, a lack of differences in inner ear bulk and cell-specific Na+/K+-ATPase and vacuolar type H+-ATPase protein abundance localization pointed out to activation of preexisting ATPases, non-bicarbonate pH buffering, or both, as the mechanism for endolymph pH-regulation. These results provide the first direct evidence showcasing the acid-base chemistry of the endolymph of OA-exposed fish favors otolith overgrowth, and suggests that this phenomenon will be more pronounced in species that count with more robust blood and endolymph pH regulatory mechanisms.
Ligand-induced changes in dynamics mediate long-range allostery in thelacrepressor
Authors: Glasgow Anum , Hobbs Helen T. , Perry Zion R. , Marqusee Susan , Kortemme Tanja 
Published: December 2021

AbstractAllostery, broadly defined as a protein’s functional response to distal perturbations, is fundamental to biological regulation. In classical models, allosteric ligand binding produces a defined set of structural changes in the protein, resulting in a different low-energy conformation. Proteins that undergo ligand-induced allostery with few observable structural changes therefore frustrate interpretations by classical models. Here we used hydrogen-deuterium exchange with mass spectrometry (HDX/MS) to map the allosteric effects in a paradigm ligand-responsive allosteric transcription factor, thelacrepressor (LacI). X-ray crystal structures of the core domain of LacI bound to different small molecule ligands, or the DNA operator, show less than 1.5 Å difference in the protein all-atom root-mean-square-deviation (RMSD) between any two structures. Despite this high degree of similarity among static structures, our HDX/MS experiments reveal widespread and unexpected differences in the flexibility of secondary structures in the LacI core domain in each functional state. We propose a model in which ligand binding allosterically switches the functional response of the repressor by selectively changing the dynamics of particular secondary structure elements relative to each other, shifting the conformational ensemble of the protein between mutually incompatible DNA-bound and inducer-bound states. Our model also provides a mechanistic context for the altered functions of thousands of documented LacI mutants. Furthermore, our approach provides a platform for characterizing and engineering allosteric responses in proteins.
Nanoscale structural organization and stoichiometry of the budding yeast kinetochore
Authors: Cieslinski Konstanty , Wu Yu-Le , Nechyporenko Lisa , Hörner Sarah Janice , Conti Duccio , Skruzny Michal , Ries Jonas 
Published: December 2021

AbstractProper chromosome segregation is crucial for cell division. In eukaryotes, this is achieved by the kinetochore, an evolutionarily conserved multi-protein complex that physically links the DNA to spindle microtubules and takes an active role in monitoring and correcting erroneous spindle-chromosome attachments. Our mechanistic understanding of these functions and how they ensure an error-free outcome of mitosis is still limited, partly because we lack a comprehensive understanding of the kinetochore structure in the cell. In this study, we use single-molecule localization microscopy to visualize individual kinetochore complexesin situin budding yeast. For major kinetochore proteins, we measured their abundance and position within the metaphase kinetochore. Based on this comprehensive dataset, we propose a quantitative model of the budding yeast kinetochore. While confirming many aspects of previous reports based on bulk imaging, our results present a unifying nanoscale model of the kinetochore in budding yeast.
A novel PSII photosynthetic control is activated in anoxic cultures of green algae
Authors: Milrad Yuval , Nagy Valéria , Tóth Szilvia Z. , Yacoby Iftach 
Published: December 2021

AbstractPhotosynthetic green algae face an ever-changing environment of fluctuating light as well as unstable oxygen levels, which via the production of free radicals constantly challenges the integrity of the photosynthetic complexes. To face such challenges, a complex photosynthetic control network monitors and tightly control the membrane redox potential. Here, we show that not only that the photosynthetic control set the rate limiting step of photosynthetic linear electron flow, but also, upon its ultimate dissipation, it triggers intrinsic alternations in the activity of the photosynthetic complexes. These changes have a grave and prolonged effect on the activity of photosystem II, leading to a massive 3-fold decrease in its electron output. We came into this conclusion via studying a variety of green algae species and applying advance mass-spectrometry and diverse spectroscopic techniques. Our results shed new light on the mechanism of photosynthetic regulation, and provide new target for improving photosynthesis.
Understanding the motivational values for the usage of specific online news media and users’ perception of information credibility
Authors: Amosun Tunde Simeon , Jianxun Chu , Rufai Olayemi Hafeez , Sayibu Muhideen , Shahani Riffat , Nadege Muhimpundu , Olaiya Tolulope B. 
Published: December 2021

Purpose
The purpose of this study is to investigate the utilitarian value (UV), hedonic value (HV) and social value (SV) that make people use a certain type of online media website and how the usage of specific online media website impact the way people perceive online information credibility (OIC). A research model was also proposed to explain the essence of this study.

Design/methodology/approach
This study adopted the survey research methodology to empirically test the research model with 873 research participants from the University of Science and Technology of China and Anhui Medical University.

Findings
Results from structural equation modeling showed that UV and HV have a significant positive impact on the usage of print news media website (PNMW), usage of broadcast news media website (BNMW) and usage of social networking website (SNW). The SV was also found to have a significant positive impact on the usage of SNWs. The result also indicated that the usage of the PNMW and the usage of the BNMW by online users have a significantly positive impact on high rating of OIC. However, the result showed that the usage of SNW does not have a significant positive impact on the high rating of OIC.

Originality/value
Findings in this study provided substantial contributions toward the advancement of the uses and gratification theoretical framework by unraveling how certain motivational values can influence online media users’ preferences for specific online media websites, as well as showing how specific online media websites affect online users’ perception of OIC.