bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the structure and self-assembly of two distinct class IB hydrophobins
Authors: Kenward Calem , Vergunst Kathleen L. , Langelaan David N. 
Published: August 2022

AbstractHydrophobins are small proteins secreted by fungi that accumulate at interfaces, modify surface hydrophobicity, and self-assemble into large amyloid-like structures. These unusual properties make hydrophobins an attractive target for commercial applications as emulsifiers and surface modifying agents. Hydrophobins have diverse sequences and tertiary structures, complicating attempts to characterize how they function. Here we describe the atomic resolution structure of the unusual hydrophobin SLH4 and compare its function to another hydrophobin, SC16. Despite containing only one charged residue, SLH4 has a similar structure to SC16 yet has strikingly different rodlet morphology and propensity to self-assemble. Secondary structure analysis of both SC16 and SLH4 before and after assembly suggest that residues in the first intercysteine loop undergo conformational changes. This work outlines a representative structure for class IB hydrophobins and illustrates how hydrophobin surface properties govern self-assembly, which provides context to rationally select hydrophobins for applications as surface modifiers.Keypoints-The atomic-resolution structure of the hydrophobin SLH4 was determined using nuclear magnetic resonance spectroscopy-The structure of SLH4 outlines a representative structure for class IB hydrophobins-The assembly characteristics of SLH4 and SC16 are strikingly different, outlining how surface properties of hydrophobins influence their function.
A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference
Authors: Puritz Jonathan B. , Guo Ximing , Hare Matt , He Yan , Hillier LaDeana , Jin Shubo , Liu Ming , Lotterhos Katie , Minx Pat , Modak Tejashree , Proestou Dina , Rice Edward S. , Tomlinson Chad , Warren Wes , Witkop Erin , Zhao Honggang , Gomez-Chiarri Marta 
Published: August 2022

AbstractGenome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster,Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed apost hocmethod to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig-masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.
Super-resolution imaging reveals dynamic reticular cytoophidia
Authors: Fang Yifan , Li Yi-Lan , Li Xiao-Ming , Liu Ji-Long 
Published: August 2022

AbstractCTP synthase (CTPS) can form filamentous structures termed cytoophidia in cells from all three domains of life. In order to study the mesoscale structure of cytoophidia, we perform fluorescence recovery after photobleaching (FRAP) and stimulated emission depletion (STED) microscopy in human cells. By using EGFP dimeric tag, as a tool to explore the physical properties of cytoophidia, we find that cytoophidia are dynamic and reticular. The reticular structure of CTPS cytoophidia may provide space for other components such as IMPDH. In addition, we observe CTPS granules with tentacles.
Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: the SH2 domain of SH2B1
Authors: Fowler Nicholas J. , Albalwi Marym F. , Lee Subin , Hounslow Andrea M. , Williamson Mike P. 
Published: August 2022

AbstractProtein structures calculated using NMR data are less accurate and less well defined than they could be. Here we use the program ANSURR to show that this deficiency is at least in part due to a lack of hydrogen bond restraints. We then describe a protocol to introduce hydrogen bond restraints into the structure calculation of the SH2 domain from SH2B1 in a systematic and transparent way, and show that the structures generated are more accurate and better defined as a result. We also show that ANSURR can be used as a guide to know when the structure calculation is good enough to stop.
Effect of beneficial sweeps and background selection on genetic diversity in changing environments
Authors: Kaushik Sachin 
Published: August 2022

AbstractNeutral theory predicts that the genetic diversity within a population is proportional to the census population size. In contrast, observed genetic diversity for various species is much lower than theoretical prediction (Lewontin’s paradox). The selective sweeps and background selection, reduce the genetic variation at the linked neutral sites and have been studied considering the environment to be selectively constant. However, in a natural population, the selective environment varies with time. Here, we investigate the impact of selective sweeps and background selection on neutral genetic diversity when the selection coefficient changes periodically over time. The reduction in genetic variation due to selective sweeps is known to depend on the conditional fixation time. Here, we find that the effect of changing environment on conditional mean fixation time is most substantial for the randomly mating population than the inbreeding population with arbitrary inbreeding coefficient. We also study the effect of background selection on neutral sites when the selection co-efficient of linked deleterious mutation change periodically in time. In the slowly changing environment, we find that neutral heterozygosity is significantly different, and the site frequency spectrum has a different shape than that in the static environment.
In vivo visualization of nitrate dynamics using a genetically encoded biosensor
Authors: Chen Yen-Ning , Cartwright Heather , Ho Cheng-Hsun 
Published: August 2022

AbstractNitrate (NO3-) uptake and distribution are critical to plant life. Although the upstream regulation of nitrate uptake and downstream responses to nitrate in a variety of cells have been well-studied, it is still not possible to directly visualize the spatial and temporal distribution of nitrate with high resolution at the cellular level. Here, we report a nuclear-localized, genetically encoded biosensor, nlsNitraMeter3.0, for the quantitative visualization of nitrate distribution in Arabidopsis thaliana. The biosensor tracked the spatiotemporal distribution of nitrate along the primary root axis and disruptions by genetic mutation of transport (low nitrate uptake) and assimilation (high nitrate accumulation). The developed biosensor effectively monitors nitrate concentrations at cellular level in real time and spatiotemporal changes during the plant life cycle.One-Sentence SummaryA genetically encoded biosensor for in vivo visualization of spatiotemporal nitrate levels at a cellular resolution.
The evo-MOTiF pipeline and database for studying protein motif evolution in a structural context
Authors: de Boissier Paul , Zweig Nathanael , Habermann Bianca H. 
Published: August 2022

AbstractShort linear motifs (SLiMs) in proteins are short functionally independent sequence stretches with a defined function and required for proteins to interact with their environment. Their functional importance makes it interesting to analyse SLiM features further, such as their structural or evolutionary properties, to understand better how SLiMs evolve to shape protein functions.We developed an automated pipeline to analyse features of SLiMs, called evo-MOTiF. This pipeline takes as input a single protein sequence and its associated SLiM(s) and returns a set of scores associated with SLiM features, including their disorder, as well as their overall, positional and amino acid property conservation. To store and easily mine data from the evo-MOTiF pipeline, we developed the evo-MOTiF database, which currently holds ∼9500 motifs, combining data from ELM, PhosphoSitePlus, as well as from cross-linking mass-spectrometry (XL-MS) experiments. The evo-MOTiF database distinguishes itself further by allowing effortless filtering for SLiMs with specific properties, such as disorder, or conservation in evolution and by providing evolutionary, as well as structural information for SLiMs. Preliminary analysis of SLiM features reveals weak negative correlation between disorder and overall, positional, as well as amino acid property conservation, which is in support of previous observations on smaller datasets.The evo-MOTiF pipeline and database are freely available athttps://gitlab.com/habermann_lab/slimsandhttp://etnadb.ibdm.univ-mrs.fr/index.php, respectively.
OHP2 is not required for psbA translation in Chlamydomonas
Authors: Wang Fei , Dischinger Korbinian , Westrich Lisa Désirée , Meindl Irene , Egidi Felix , Trösch Raphael , Sommer Frederik , Johnson Xenie , Schroda Michael , Nickelsen Joerg , Willmund Felix , Vallon Olivier , Bohne Alexandra-Viola 
Published: August 2022

ABSTRACTIn land plants and cyanobacteria, co-translational association of chlorophyll (Chl) to the nascent D1 polypeptide, a reaction center protein of photosystem II (PSII), requires a Chl binding complex consisting of a short-chain dehydrogenase (HCF244/Ycf39) and One-Helix Proteins of the LHC superfamily (OHP1 and OHP2 in chloroplasts). Here, we show that an ohp2 mutant of the green alga Chlamydomonas reinhardtii fails to accumulate core PSII subunits, in particular D1. Extragenic suppressors arise at high frequency, suggesting the existence of another route for Chl association to PSII. The ohp2 mutant can be complemented by the Arabidopsis ortholog. In contrast to land plants, where psbA translation is prevented in the absence of OHP2, ribosome profiling experiments show that the Chlamydomonas mutant translates the psbA transcript over its full length. Pulse labelling suggests that D1 is degraded during or immediately after translation. The translation of other PSII subunits is affected by assembly-controlled translational regulation (the CES process). Proteomics show that HCF244, a translation factor which associates with and is stabilized by OHP2 in land plants, still partly accumulates in the Chlamydomonas ohp2 mutant, explaining the persistence of psbA translation. Several Chl biosynthesis enzymes overaccumulate in the mutant membranes. Partial inactivation of the D1-degrading FtsH protease restores a low level of PSII activity in an ohp2 background, but not photoautotrophy. Taken together, our data suggest that OHP2 is not required for psbAD1 translation in Chlamydomonas, but necessary for its stabilization.
A Small Subset of Cytosolic dsRNAs Must Be Edited by ADAR1 to Evade MDA5-Mediated Autoimmunity
Authors: Sun Tao , Li Qin , Geisinger Jonathan M. , Hu Shi-Bin , Fan Boming , Su Shichen , Tsui Waitang , Guo Hongchao , Ma Jinbiao , Li Jin Billy 
Published: August 2022

AbstractThe innate immune system detects viral infection via pattern recognition receptors and induces defense reactions such as production of type I interferon1. One such receptor, MDA5, is activated upon the recognition of double-stranded RNAs (dsRNAs) that are often produced during viral replication2. Endogenous dsRNAs evade MDA5 activation through RNA editing by ADAR1, thus preventing autoimmunity3-5. Among the large number of endogenous dsRNAs, the key substrates whose editing is critical to evade MDA5 activation (termed as immunogenic dsRNAs) remain elusive. Here we reveal the identity of human immunogenic dsRNAs, a surprisingly small fraction of all cellular dsRNAs, to fill the gap in the ADAR1-dsRNA-MDA5 axis. We found that, in contrast to previous findings6,7, the immunogenic dsRNAs were highly enriched in mRNAs and depleted of introns, an expected indication of bona fide substrates of cytosolic MDA5. The immunogenic dsRNAs, in contrast to non-immunogenic dsRNAs, tended to have shorter loop between the stems, which may facilitate dsRNA formation. They also tended to be enriched at the GWAS signals of common inflammatory diseases, implying that they are truly immunogenic. We validated the MDA5-dependent immunogenicity of the dsRNAs, which was dampened following ADAR1-mediated RNA editing. We anticipate that a focused analysis of immunogenic dsRNAs will greatly facilitate the understanding and treatment of cancer and inflammatory diseases in which the important roles of dsRNA editing and sensing continue to be revealed8-13.
Reduced methionine synthase (Mtr) expression creates a functional vitamin B12 deficiency that leads to uracil accumulation in mouse mitochondrial DNA
Authors: Heyden Katarina E. , Fiddler Joanna L. , Xiu Yuwen , Malysheva Olga V. , Handzlik Michal K. , Phinney Whitney N. , Stiles Linsey , Stabler Sally S. , Metallo Christian M. , Caudill Marie A. , Field Martha S. 
Published: August 2022

AbstractAdequate thymidylate (dTMP or the “T” base in DNA) levels are essential for stability of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). Folate and vitamin B12 (B12) are essential cofactors in folate-mediated one carbon metabolism (FOCM), a metabolic network which supports synthesis of nucleotides (including dTMP) and methionine. Perturbations in FOCM impair dTMP synthesis, causing misincorporation of uracil (or a “U” base) into DNA. During B12 deficiency, cellular folate accumulates as 5-methyltetrahdryfolate (5-methyl-THF), limiting nucleotide synthesis. The purpose of this study was to determine how B12 deficiency and dietary folate interact to affect mtDNA integrity and mitochondrial function in mouse liver. Mice expressing reduced methionine synthase (Mtr) levels were used to create a functional B12 deficiency. Folate accumulation, uracil levels, mtDNA content, and oxidative phosphorylation capacity were measured in male Mtr+/+ and Mtr+/- mice weaned onto either a folate-sufficient control diet (2 mg/kg folic acid, C) or a folate-deficient diet (FD, lacking folic acid) for 7 weeks. Mtr heterozygosity led to increased liver 5-methyl-THF levels. Mtr+/- mice consuming the C diet also exhibited a 40-fold increase in uracil in liver mtDNA. However, the combination of Mtr heterozygosity and exposure to the FD diet partially alleviated the level of uracil accumulation in mtDNA. Furthermore, Mtr+/- mice exhibited a 25% decrease in liver mtDNA content and a 20% decrease in maximal oxygen consumption rates. Impairments in mitochondrial FOCM are known to lead to increased uracil in mtDNA. This study demonstrates that impaired cytosolic dTMP synthesis also leads to increased uracil in mtDNA.
Structure of angiogenin dimer bound to double-stranded RNA
Authors: Sievers Katharina , Ficner Ralf 
Published: August 2022

Angiogenin is an unusual member of the RNase A family and is of great interest in multiple pathological contexts. Although it has been assigned various regulatory roles, its core catalytic function is that of an RNA endonuclease. However, its catalytic efficiency is comparatively low and this has been linked to a unique C-terminal helix which partially blocks its RNA-binding site. Assuming that binding to its RNA substrate could trigger a conformational rearrangement, much speculation has arisen on the topic of the interaction of angiogenin with RNA. To date, no structural data on angiogenin–RNA interactions have been available. Here, the structure of angiogenin bound to a double-stranded RNA duplex is reported. The RNA does not reach the active site of angiogenin and no structural arrangement of the C-terminal domain is observed. However, angiogenin forms a previously unobserved crystallographic dimer that makes several backbone interactions with the major and minor grooves of the RNA double helix.
A C2 continuous trajectory planning method for 6-DOF rotational robot manipulators
Authors: Min Kang , Ni Fenglei , Zhang Guojun , Shu Xin , Liu Hong 
Published: August 2022

Purpose
The purpose of this paper is to propose a smooth double-spline interpolation method for six-degree-of-freedom rotational robot manipulators, achieving the global C2 continuity of the robot trajectory.

Design/methodology/approach
This paper presents a smooth double-spline interpolation method, achieving the global C2 continuity of the robot trajectory. The tool center positions and quaternion orientations are first fitted by a cubic B-spline curve and a quartic-polynomial-based quaternion spline curve, respectively. Then, a parameter synchronization model is proposed to realize the synchronous and smooth movement of the robot along the double spline curves. Finally, an extra u-s function is used to record the relationship between the B-spline parameter and its arc length parameter, which may reduce the feed rate fluctuation in interpolation. The seven segments jerk-limited feed rate profile is used to generate motion commands for algorithm validation.

Findings
The simulation and experimental results demonstrate that the proposed method is effective and can generate the global C2-continuity robot trajectory.

Originality/value
The main contributions of this paper are as follows: guarantee the C2 continuity of the position path and quaternion orientation path simultaneously; provide a parameter synchronization model to realize the synchronous and smooth movement of the robot along the double spline curves; and add an extra u-s function to realize arc length parameterization of the B-spline path, which may reduce the feed rate fluctuation in interpolation.
Human vs robot baristas during the COVID-19 pandemic: effects of masks and vaccines on perceived safety and visit intention
Authors: Choi Miju , Choi Youngjoon , Kim Seongseop (Sam) , Badu-Baiden Frank 
Published: August 2022

Purpose
This study aims to compare the effect of barista type (human vs robot) on perceived safety and examine the role of two moderators (mask-wearing and coronavirus vaccination) on the effects of barista type on perceived safety and visit intention.

Design/methodology/approach
The research design consists of three studies. Three experiments were sequentially designed and conducted to address research questions.

Findings
Study 1 found that perceived safety mediates the effect of barista type on customers’ visit intention. Study 2 revealed that the mask-wearing of human and robot baristas differently influences perceived safety. Study 3 showed that customers, especially where robot baristas are used, perceive the effect of mask-wearing differently depending on their coronavirus vaccination status.

Research limitations/implications
Given that the levels of restrictions vary worldwide, together with the extent of countries’ vaccination rollouts, caution is required when generalising the research findings.

Practical implications
The findings have practical implications for the hospitality industry, where the roles of face masks and coronavirus vaccines in shaping consumer psychology and behaviour have been underexplored.

Originality/value
Coronavirus vaccination is considered one of the most important driving forces for the recovery of hospitality businesses. As a heuristic-systematic model postulated, this study identified that vaccination status (fully vaccinated vs not vaccinated) changes the level of involvement when customers assess the level of risk in service environments. By pinpointing the function of service robots in safeguarding customers from the potential spread of the disease, this study broadens the scope of human–robot interaction research in hospitality.
Culture, language, and accounting reform: a new perspective on IPSAS implementation
Authors: Abdulkarim Mustafa Elkasih , Umlai Mohamed Ismail , Al-Saudi Layth Faris 
Published: August 2022

Purpose
This study aims to explore the role that culture and language play in the implementation of International Public Sector Accounting Standards (IPSAS).

Design/methodology/approach
The Hofstede–Gray and Huerta et al. (2013) models were used to collect data on language and accounting culture. Paired-sample t-test, regression and factor analyses were conducted on data from a sample of 101 respondents. This study also used ordinary least squares to test hypotheses.

Findings
The cultural dimensions of professionalism, secrecy and uniformity significantly influence the implementation of IPSAS. Furthermore, this study finds a significant link between culture, language and IPSAS implementation, which underlines the need for careful consideration of International Public Sector Accounting Standards Board policies in the promotion of IPSAS internationally.

Research limitations/implications
While this study is limited to its research method, using secondary data would have been challenging given the setting and accessibility issues. This study overcomes this problem by using a self-administered questionnaire. Prior studies confirm the reliability of the constructs. Despite providing justifications for why the authors use judgemental sampling, the authors acknowledge the limitation of the technique in survey distribution. Furthermore, the findings cannot be read without caution, as the authors focused on one country. However, interactions between accounting practices and culture in one country may be transferred to other countries that share a common language and culture with Qatar. The authors believe future research in this area will complement the understanding of the determinants of IPSAS implementation should the study be replicated.

Social implications
Policymakers, standard setters and regulators should promote and enforce an integrated approach that reflects the need for accountants and auditors to be conscious of the effects of culture and language, given the likelihood of widespread IPSAS adoption.

Originality/value
This study offers insight into the significance of culture and language in reforming public-sector accounting systems in developing nations and emerging economies.