bluuebunny/crossref_metadata_2025_split huggingface dataset:
Illuminating the mechanism and allosteric behavior of NanoLuc luciferase
Authors: Nemergut Michal , Pluskal Daniel , Horackova Jana , Sustrova Tereza , Tulis Jan , Barta Tomas , Baatallah Racha , Gagnot Glwadys , Novakova Veronika , Majerova Marika , Sedlackova Karolina , Marques Sérgio M. , Toul Martin , Damborsky Jiri , Prokop Zbynek , Bednar David , Janin Yves L. , Marek Martin 
Published: December 2022

AbstractNanoLuc, a superior β-barrel fold luciferase, was engineered 10 years ago but the nature of its catalysis remains puzzling. Here experimental and computational techniques were combined, revealing that imidazopyrazinone luciferins bind to an intra-barrel catalytic site but also to an allosteric site shaped on the enzyme surface. Structurally, binding to the allosteric site prevents simultaneous binding to the catalytic site, andvice versa, through concerted conformational changes. We demonstrate that restructuration of the allosteric site can boost the luminescent reaction in the remote active site. Mechanistically, an intra-barrel arginine coordinates the imidazopyrazinone component of luciferin, which reacts with O2via a radical charge-transfer mechanism, and then it also protonates the resulting excited amide product to form a light-emitting neutral species. Concomitantly, an aspartate, supported by two tyrosines, fine-tunes the blue color emitter to secure a high emission intensity. This information is critical to engineering the next-generation of ultrasensitive bioluminescent reporters.
Processing of the hepatitis E virus polyprotein can be mediated by a cellular protease
Authors: Pierce Danielle M. , Buchanan Frazer J.T. , Cox Abigail , Abualsaoud Khadijah , Ward Joseph C. , Harris Mark , Stonehouse Nicola J. , Herod Morgan R. 
Published: December 2022

AbstractThe genomes of positive-sense RNA viruses encode polyproteins that are essential for controlling viral replication. These viral polyproteins must undergo proteolysis (also termed polyprotein processing) to generate functional protein units. This proteolysis can be performed by virally-encoded proteases as well as host cellular proteases, and is generally believed to be a key step in regulating viral replication. Hepatitis E virus (HEV), a leading cause of acute viral hepatitis, translates its positive-sense RNA genome to generate a polyprotein, termed pORF1, which is necessary and sufficient for viral genome replication. However, the mechanism of polyprotein processing in HEV remains to be determined. In this study, we aimed to understand processing of this polyprotein and its role in viral replication using a combination ofin vitrotranslation experiments and HEV sub-genomic replicons.Our data suggest no evidence for a virally-encoded protease or auto-proteolytic activity asin vitrotranslation predominantly generates unprocessed viral polyprotein precursors. However, seven cleavage sites within the polyprotein (suggested by bioinformatic analysis) are susceptible to the host cellular protease, thrombin. Using a sub-genomic replicon system, we demonstrate that mutagenesis of these sites prevents replication, as does pharmacological inhibition of serine proteases. Overall, our data supports a model where HEV uses host proteases to support its replication and could have uniquely evolved not to rely on a virally-encoded protease for replication.Author summaryPositive-strand RNA viruses produce polyproteins that are cleaved by proteases that control viral replication. The polyproteins of all well studied positive-strand viruses undergo proteolysis in a highly controlled manner to generate functional proteins and regulate the transition from translation to RNA replication. Proteolysis of viral polyproteins is generally performed by virally-encoded proteases, although host cell proteases are used by some viruses. In this report, we provide evidence that suggests that hepatitis E virus, a medically important human pathogen, does not encode a protease and unlike other viral polyproteins cannot undergo auto-catalytic processing. Instead, we provide evidence that the polyprotein is susceptible to proteolysis by host cell proteases and that this is essential for viral replication. Our data contradict the previous dogma of positive-sense viral replication and suggests a model where this virus has evolved to use a host protease to control viral replication and tropism.
Dynamin A as a one-component division machinery for synthetic cells
Authors: De Franceschi Nicola , Barth Roman , Meindlhumer Sabrina , Fragasso Alessio , Dekker Cees 
Published: December 2022

AbstractMembrane abscission, the final cut of the last connection between emerging daughter cells, is an indispensable event in the last stage of cell division, as well as in other cellular processes such as endocytosis, virus release, or bacterial sporulation. However, its mechanism remains poorly understood, which also impedes its application as a cell-division machinery for synthetic cells. Here, we use fluorescence microscopy and Fluorescence Recovery After Photobleaching (FRAP) to study thein vitroreconstitution of the bacterial protein Dynamin A (DynA) inside liposomes. Upon external reshaping of the liposomes into dumbbells, DynA self-assembles at the membrane neck, resulting in membrane hemi-scission and even full scission. DynA proteins constitute a simple one-component division machinery that is capable of splitting dumbbell-shaped liposomes, marking an important step towards building a synthetic cell.
The canonical E2Fs together with RETINOBLASTOMA-RELATED are required to establish quiescence during plant development
Authors: Gombos Magdolna , Raynaud Cécile , Nomoto Yuji , Molnár Eszter , Brik-Chaouche Rim , Takatsuka Hirotomo , Zaki Ahmad , Bernula Dóri , Latrasse David , Mineta Keito , Nagy Fruzsina , He Xiaoning , Iwakawa Hidekazu , Őszi Erika , An Jing , Suzuki Takamasa , Papdi Csaba , Bergis Clara , Benhamed Moussa , Bögre László , Ito Masaki , Magyar Zoltán 
Published: December 2022

AbstractMaintaining stable and transient quiescence in differentiated and stem cells, respectively, requires repression of the cell cycle. The plant RETINOBLASTOMA-RELATED (RBR) has been implicated in stem cell maintenance, presumably by forming repressor complexes with E2F transcription factors. Surprisingly we find that mutations in all three canonical E2Fs do not compromise the cell cycle, but similarly toRBRsilencing, result in overproliferation. Contrary to the growth arrest upon RBR silencing, when exit from proliferation to differentiation is inhibited, thee2fabcmutant develops enlarged organs with supernumerary stem and differentiated cells as the quiescence is compromised. While E2F, RBR and the M-phase regulatory MYB3Rs are part of the DREAM repressor complexes, and recruited to overlapping groups of targets, they regulate distinct sets of genes. Only the loss of E2Fs but not the MYB3Rs interferes with quiescence, which might be due to the ability of E2Fs to control both G1-S and some key G2-M targets. We conclude that collectively the three canonical E2Fs in complex with RBR have central roles in establishing cellular quiescence during organ development, leading to enhanced plant growth.
DiffDomain enables identification of structurally reorganized topologically associating domains
Authors: Hua Dunming , Gu Ming , Zhang Xiao , Du Yanyi , Xie Hangcheng , Qi Li , Du Xiangjun , Bai Zhidong , Zhu Xiaopeng , Tian Dechao 
Published: December 2022

AbstractTopologically associating domains (TADs) are critical structural units in three-dimensional genome organization of mammalian genome. Dynamic reorganizations of TADs between health and disease states are associated with transcription and other essential genome functions. However, computational methods that can identify reorganized TADs are still in the early stages of development. Here, we present DiffDomain, an algorithm leveraging high-dimensional random matrix theory to identify structurally reorganized TADs using chromatin contact maps. Method comparison using multiple real Hi-C datasets reveals that DiffDomain outperforms alternative methods for FPRs, TPRs, and identifying a new subtype of reorganized TADs. The robustness of DiffDomain and its biological applications are demonstrated by applying on Hi-C data from different cell types and disease states. Identified reorganized TADs are associated with structural variations and changes in CTCF binding sites and other epigenomic changes. By applying to a single-cell Hi-C data from mouse neuronal development, DiffDomain can identify reorganized TADs between cell types with reasonable reproducibility using pseudo-bulk Hi-C data from as few as 100 cells per condition. Moreover, DiffDomain reveals that TADs have differential cell-to-population variability and heterogeneous cell-to-cell variability. Therefore, DiffDomain is a statistically sound method for better comparative analysis of TADs using both Hi-C and single-cell Hi-C data.
Cyclic lipopeptides as membrane fusion inhibitors against SARS-CoV-2: new tricks for old dogs
Authors: Shekunov Egor V. , Zlodeeva Polina D. , Efimova Svetlana S. , Muryleva Anna A. , Zarubaev Vladimir V. , Slita Alexander V. , Ostroumova Olga S. 
Published: December 2022

AbstractWith the resurgence of the coronavirus pandemic, the repositioning of FDA-approved drugs against coronovirus and finding alternative strategies for antiviral therapy are both important. We previously identified the viral lipid envelope as a potential target for the prevention and treatment of SARS-CoV-2 infection with plant alkaloids [1]. Here, we investigated the effects of eleven cyclic lipopeptides (CLPs), including well-known antifungal and antibacterial compounds, on the liposome fusion triggered by calcium, polyethylene glycol 8000, and a fragment of SARS-CoV-2 fusion peptide (816-827) by calcein release assays. Differential scanning microcalorimetry of the gel-to-liquid-crystalline and lamellar-to-inverted hexagonal phase transitions and confocal fluorescence microscopy demonstrated the relation of the fusion inhibitory effects of CLPs to alterations in lipid packing, membrane curvature stress and domain organization. The effects of the compounds were evaluated in anin vitro Vero-based cell model, and aculeacin A, anidulafugin, iturin A, and mycosubtilin attenuated the cytopathogenicity of SARS-CoV-2 without specific toxicity.
A multi-channel electrophysiology approach to non-invasively and precisely record human spinal cord activity
Authors: Nierula Birgit , Stephani Tilman , Bailey Emma , Kaptan Merve , Pohle Lisa-Marie , Horn Ulrike , Mouraux André , Maess Burkhard , Villringer Arno , Curio Gabriel , Nikulin Vadim V. , Eippert Falk 
Published: December 2022

AbstractThe spinal cord is of fundamental importance for integrative processing in brain-body communication, yet routine non-invasive recordings in humans are hindered by vast methodological challenges. Here we overcome these challenges by developing an easy-to-use electrophysiological approach based on high-density multi-channel spinal recordings combined with multivariate spatial-filtering analyses. These advances enable a spatiotemporal characterization of spinal cord responses and demonstrate a sensitivity that permits assessing even single-trial responses. To furthermore enable the study of integrative processing along the neural processing hierarchy in somatosensation, we expand this approach by simultaneous peripheral, spinal and cortical recordings and provide direct evidence that bottom-up integrative processing occurs already within the spinal cord and thus after the first synaptic relay in the central nervous system. Finally, we demonstrate the versatility of this approach by providing non-invasive recordings of nociceptive spinal cord responses during heat-pain stimulation. Beyond establishing a new window on human spinal cord function at millisecond timescale, this work provides the foundation to study brain-body communication in its entirety in health and disease.
X-Chromosome Target Specificity Diverged Between Dosage Compensation Mechanisms of Two Closely RelatedCaenorhabditisSpecies
Authors: Yang Qiming , Lo Te-Wen , Brejc Katjuša , Schartner Caitlin , Ralston Edward J. , Lapidus Denise M. , Meyer Barbara J. 
Published: December 2022

AbstractAn evolutionary perspective enhances our understanding of biological mechanisms. Comparison of sex determination and X-chromosome dosage compensation mechanisms between the closely related nematode speciesC. briggsae(Cbr) andC. elegans(Cel) revealed that the genetic regulatory hierarchy controlling both processes is conserved, but the X-chromosome target specificity and mode of binding for the specialized condensin dosage compensation complex (DCC) controlling X expression have diverged. We identified two motifs withinCbrDCC recruitment sites that are highly enriched on X: 13-bp MEX and 30-bp MEX II. Mutating either MEX or MEX II in an endogenous recruitment site with multiple copies of one or both motifs reduced binding, but only removing all motifs eliminated bindingin vivo. Hence, DCC binding toCbrrecruitment sites appears additive. In contrast, DCC binding toCelrecruitment sites is synergistic: mutating even one motifin vivoeliminated binding. Although all X-chromosome motifs share the sequence CAGGG, they have otherwise diverged so that a motif from one species cannot function in the other. Functional divergence was demonstratedin vivoandin vitro. A single nucleotide position inCbrMEX can determine whetherCelDCC binds. This rapid divergence of DCC target specificity could have been an important factor in establishing reproductive isolation between nematode species and contrasts dramatically with conservation of target specificity for X-chromosome dosage compensation acrossDrosophilaspecies and for transcription factors controlling developmental processes such as body-plan specification from fruit flies to mice.
Pre-epidemic evolution of the USA300 clade and a molecular key for classification
Authors: Bianco Colleen , Moustafa Ahmed M. , O’Brien Kelsey , Martin Michael , Read Timothy D. , Kreiswirth Barry , Planet Paul J. 
Published: December 2022

AbstractUSA300 has remained the dominant community and healthcare associated methicillin-resistantStaphylococcus aureus(MRSA) clone in the United States and in northern South America for at least the past 20 years. In this time, it has experienced epidemic spread in both of these locations. However, its pre-epidemic evolutionary history and origins are incompletely understood. Large sequencing databases, such as NCBI, PATRIC, and Staphopia, contain clues to the early evolution of USA300 in the form of sequenced genomes of USA300 isolates that are representative of lineages that diverged prior to the establishment of the South American (SAE) and North American (NAE) epidemics. In addition, historical isolates collected prior to the emergence of epidemics can help reconstruct early events in the history of this lineage. Here, we take advantage of the accrued, publicly available data, as well as two newly sequenced pre-epidemic historical isolates from 1996, and a very early diverging ACME-negative NAE genome to understand the pre-epidemic evolution of USA300. We use database mining techniques to emphasize genomes similar to pre-epidemic isolates, with the goal of reconstructing the early molecular evolution of the USA300 lineage. Phylogenetic analysis with these genomes confirms that the North American Epidemic and South American Epidemic USA300 lineages diverged from a most recent common ancestor around 1970 with high confidence, and it also pinpoints the independent acquisition events of the of the ACME and COMER loci with greater precision than in previous studies. We solidify evidence for a North American origin of the USA300 lineage and identify multiple introductions of USA300 into South America from North America. Notably, we describe a third major USA300 clade (the pre-epidemic branching clade; PEB1) consisting of both MSSA and MRSA isolates circulating around the world that diverged from the USA300 lineage prior to the establishment of the South American and North American epidemics. We present a detailed analysis of specific sequence characteristics of each of the major clades, and present diagnostic positions that can be used to classify new genomes.
Effects of continuous tactile stimulation on auditory-evoked cortical responses depend on the audio-tactile phase
Authors: Fu Xueying , Riecke Lars 
Published: December 2022

AbstractAuditory perception can benefit from stimuli in non-auditory sensory modalities, as for example in lip-reading. Compared with such visual influences, tactile influences are still poorly understood. It has been shown that single tactile pulses can enhance the perception of auditory stimuli depending on their relative timing, but whether and how such brief auditory enhancements can be stretched in time with more sustained, phase-specific periodic tactile stimulation is still unclear. To address this question, we presented tactile stimulation that fluctuated coherently and continuously at 4Hz with an auditory noise (either in-phase or anti-phase) and assessed its effect on the cortical processing and perception of an auditory signal embedded in that noise. Scalp-electroencephalography recordings revealed an enhancing effect of in-phase tactile stimulation on cortical responses phase-locked to the noise and a suppressive effect of anti-phase tactile stimulation on responses evoked by the auditory signal. Although these effects appeared to follow well-known principles of multisensory integration of discrete audio-tactile events, they were not accompanied by corresponding effects on behavioral measures of auditory signal perception. Our results indicate that continuous periodic tactile stimulation can enhance cortical processing of acoustically-induced fluctuations and mask cortical responses to an ongoing auditory signal. They further suggest that such sustained cortical effects can be insufficient for inducing sustained bottom-up auditory benefits.
The pandemic readiness assessment of building design and engineering service-related legislation in Kazakhstan and the EU
Authors: Tokazhanov Galym , Tokbolat Serik , Tleuken Aidana , Karaca Ferhat 
Published: December 2022

PurposeThe current COVID-19 pandemic is influencing our life in every aspect, including working and living environments. Millions of people were forced to isolate themselves in their homes, which has posed significant pressure on buildings and shown us that our dwellings are not designed for such purposes. This is partly due to the fact that homes are designed and built for occasional use rather than isolated and long-term occupation. The legislative system of a country plays an important role in defining and shaping the conditions of people living there. Hence, the aim of the study is to evaluate the readiness of Kazakhstani and the EU construction-related legislation for pandemics.Design/methodology/approachPreviously developed pandemic-resilient indicators were used for the evaluation of construction legislation. Both legislative systems were reviewed, and the quality of responses was evaluated by assigning response scores.FindingsThe results based on response scores indicate that the environmental resource consumption sub-category was better covered by EU legislation. At the same time, the buildings’ health, safety and comfort are better taken into account in Kazakhstani legislation. Seven pandemic-resilient indicators were not responded to by any legislative system indicating a gap between current legislation and requirements for new living conditions.Originality/valueNo study has analyzed how COVID-19 can transform construction legislation. The study reveals the limitation of current construction legislation in Kazakhstan (KZ) and the EU, indicating the need for transformation to meet the requirements of the pandemic era.
Falling short of equal opportunities for persons with disabilities in Trinidad and Tobago: evidence from Equal Opportunity Commission case files
Authors: Parey Bephyer , Kutscher Elisabeth , Enightoola Hannah 
Published: December 2022

PurposeThe purpose of the study is to examine if the existing legislative framework in Trinidad and Tobago supports equal opportunities and the achievement of fundamental human rights for persons with disabilities seeking to access education, employment, accommodations and goods and services.Design/methodology/approachData were collected from 105 complaints filed with Trinidad and Tobago's Equal Opportunity Commission from 2010 to 2021 regarding disability discrimination. The steps of constant comparison were used to analyse characteristics of each case, complainants' desired outcomes and the actual outcomes of the cases (i.e. withdrawn, closed, forwarded to conciliation or the Equal Opportunity Tribunal).FindingsAcross all cases, persons with disabilities desired access to unavailable services, opportunities for employment or an apology for emotional distress. Cases that were withdrawn reflected missed opportunities to address systemic issues, closed cases reflected a bounded process for redress, and cases advancing to conciliation or the Tribunal required documentation or support.Originality/valueThis study provides insights into how the current policy and its implementation miss opportunities to address discrimination at organisational and systemic levels. Specifically, cases revealed dominant/subordinate dynamics in society and a lack of transparency throughout the system. Authors provide recommendations for policy and systemic change, including addressing gaps in national legislation and adopting strong equality of opportunity and equality of well-being approaches.
The influence of consumer religiosity on responses to rational and emotional ad appeals
Authors: Cabano Frank Gregory , Minton Elizabeth A. 
Published: December 2022

PurposeThis research aims to examine how religiosity influences consumers’ responses to rational versus emotional ad appeals.Design/methodology/approachFour experiments were conducted that examined how religiosity affected consumers’ responses (attitude toward the product, purchase intentions and brand trust) to rational versus emotional ad appeals, and how perceived fit between the ad appeal type and consumers’ information processing style mediated the effects.FindingsThe results show that consumers low in religiosity respond more favorably to rational (vs emotional) appeals because of these types of appeals being more congruent with their rational information processing style. In addition, there is no difference in consumer responses toward rational and emotional appeals for individuals high in religiosity.Research limitations/implicationsIn this research, the authors only used surveys and measured behavioral intentions rather than actual behaviors. Thus, future research should measure actual behaviors in the field to enhance the external validity of the observed effects. In addition, this research samples one primary culture that is more representative of Judeo-Christian religious beliefs. Therefore, future research should sample from other cultures and religious groups.Practical implicationsThe results suggest that marketers should use rational rather than emotional appeals in their marketing communications to low religiosity consumers (identifiable through such means as demographic data for geographic regions or self-identified classifications on social media). Marketers can also prime low religiosity in their messages (e.g. using words such as “evolution”) and, when doing so, should couple that prime with a rational (vs emotional) appeal.Originality/valueThis research is novel in that it is the first, to the best of the authors’ knowledge, to examine how religiosity influences consumers’ responses to rational versus emotional ad appeals.