bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibited KdpFABC resides in an E1 off-cycle state
Authors: Silberberg Jakob M. , Stock Charlott , Hielkema Lisa , Corey Robin A. , Rheinberger Jan , Wunnicke Dorith , Dubach Victor R. A. , Stansfeld Phillip J. , Hänelt Inga , Paulino Cristina 
Published: June 2022

AbstractKdpFABC is a high-affinity prokaryotic K+ uptake system that forms a functional chimera between a channel-like subunit (KdpA) and a P-type ATPase (KdpB). At high K+ levels, KdpFABC needs to be inhibited to prevent excessive K+ accumulation to the point of toxicity. This is achieved by a phosphorylation of the serine residue in the TGES162 motif in the A domain of the pump subunit KdpB (KdpBS162-P). Here, we explore the structural basis of inhibition by KdpBS162 phosphorylation by determining the conformational landscape of KdpFABC under inhibiting and non-inhibiting conditions. Under turnover conditions, we identified a new inhibited KdpFABC conformation that we termed E1-P tight, which is not part of the canonical Post-Albers transport cycle of P-type ATPases. It likely represents the biochemically described stalled E1-P state adopted by KdpFABC upon KdpBS162 phosphorylation. The E1-P tight state exhibits a compact fold of the three cytoplasmic domains and is likely adopted when the transition from high-energy E1-P states to E2-P states is unsuccessful. This study represents a structural characterization of a biologically relevant off-cycle state in the P-type ATPase family and supports the emerging discussion of P-type ATPase regulation by such conformations.
Cortical dynamics following real-time MEG neurofeedback training of the speed of shifting spatial attention: a pilot study
Authors: Rana Kunjan D. , Khan Sheraz , Hämäläinen Matti S. , Vaina Lucia M. 
Published: June 2022

ABSTRACTNeurofeedback is a technique that directs self-regulated modulation of neural activity. This is achieved by delivering real-time feedback derived from brain signals. In our previous work, we introduced a novel method, state-based neurofeedback (sb-NFB) that targets patterns of MEG signals related to shifts in spatial attention. In this pilot study, we used sb-NFB to train participants to decrease the time required to covertly shift spatial attention from one visual hemifield to the other. We characterized the changes to cortical connectivity during each training session. In addition, we run a separate, Posner-like validation task before the training sessions and after the training was complete. We found a significant main effect of training on the reaction time linked to switching spatial attention in both the training task and the validation task. This indicates the achieved improvement in shifting spatial attention generalized to another situation requiring this capability.
Dispersal-behavioral plasticity within an insect-host system undergoing human-induced rapid environmental change (HIREC)
Authors: Bernat Anastasia , Cenzer Meredith 
Published: June 2022

AbstractAs environments change, often drastically, due to human activities, dispersal-behavioral plasticity can become a key mediator of metapopulation connectivity and the interactions between an individual and its altered environment. Our goal was to investigate the traits and ecological processes that affect plastic dispersal responses within an insect-host system undergoing human-induced rapid evolutionary change (HIREC). Since the 1960s, populations of the red-shouldered soapberry bug from Florida, USA, originally feeding on the seeds of Cardiospermum corindum on the islands, quickly adapted to feeding on an invasive, ornamental tree, Koelreuteria elegans, on the mainland, which led to host-specific wing polyphenism. Here, we measured the morphology of >3,500 soapberry bugs field collected from 2013 to 2020 and the flight performance of 378 total soapberry bugs tested in a flight mill during Fall 2019 and Winter 2020. Flight tests showed females and mainland natives exhibited variable flight responses mediated by mass, while males were consistent, wing-dependent flyers. However, historical specimens showed annual rises in flightless morphs for males and dwindling wing-to-body sizes for island natives since 2013. Despite uncertain future fitness consequences, plasticity could help predict mobility character and agent dispersal behavior and ultimately help identify whether recent trends signal adjustment or maladaptation to HIREC.
The domain-separation low-dimensional language network dynamics in the resting-state support the flexible functional segregation and integration during language and speech processing
Authors: Yuan Binke , Xie Hui , Wang Zhihao , Xu Yangwen , Zhang Hanqing , Liu Jiaxuan , Chen Lifeng , Li Chaoqun , Tan Shiyao , Lin Zonghui , Hu Xin , Gu Tianyi , Lu Junfeng , Liu Dongqiang , Wu Jinsong 
Published: June 2022

AbstractModern linguistic theories and network science propose that the language and speech processing is organized into hierarchical, segregated large-scale subnetworks, with a core of dorsal (phonological) stream and ventral (semantic) stream. The two streams are asymmetrically recruited in receptive and expressive language or speech tasks, which showed flexible functional segregation and integration. We hypothesized that the functional segregation of the two streams was supported by the underlying network segregation. A dynamic conditional correlation approach was employed to construct frame-wise time-varying language networks and investigate the temporal reoccurring patterns. We found that the time-varying language networks in the resting-state robustly clustered into four low-dimensional states, which dynamically reconfigured following a domain-separation manner. Spatially, the hub distributions of the first three states highly resembled the neurobiology of primary auditory processing and lexical-phonological processing, motor and speech production processing, and semantic processing, respectively. The fourth state was characterized by the weakest functional connectivity and subserved as a baseline state. Temporally, the first three states appeared exclusively in limited time bins (∼15%), and most of the time (> 55%), the language network kept inactive in state 4. Machine learning-based dFC-linguistics prediction analyses showed that dFCs of the four states significantly predicted individual linguistic performance. These findings suggest a domain-separation manner of language network dynamics in the resting-state, which forms a dynamic “meta-networking” (network of networks) framework.HighlightsThe time-varying language network in the resting-state is robustly clustered into four low-dimensional states.Spatially, the first three dFC states are cognitively meaningful, which highly resemble the neurobiology of primary auditory processing and lexical-phonological representation, speech production processing, and semantic processing, respectively.Temporally, the first three states appeared exclusively in limited time bins (∼15%), and most of the time (> 55%), the language network kept inactive in state 4.A dynamic “meta-networking” framework of language network in the resting-state is proposed.
Normalization of MRI T1w between-scan effects for improved longitudinal volumetric estimates
Authors: Sederevičius Donatas , Bjørnerud Atle , Walhovd Kristine B. , Fjell Anders M. 
Published: June 2022

AbstractVariations in image intensities and contrasts between magnetic resonance imaging (MRI) acquisitions affect the subsequent image processing and its derived outcomes. Therefore, comparability between acquisitions is improved if we reduce these variations. This is especially relevant for longitudinal studies where a change of scanner or acquisition protocol often happens between subsequent examinations. In this study, we use a robust intensity distribution alignment (RIDA) method to reduce between-scan effects and improve longitudinal volume change estimates between two MRI scanners – Siemens 1.5T Avanto and 3T Skyra. The method is based on MRI T1w images acquired in close succession and robustly aligns two cumulative distribution functions of voxel intensities to harmonize image intensities and improve image-derived outcomes of a range of subcortical brain. We compare RIDA with volume-based correction - a simple linear regression model. In both cases, we derive intensity and volume transformations from a training dataset of 20 participants scanned on both scanners on the same day and apply to an independent longitudinal test dataset of 243 participants. All participants in the test set were scanned at the Avanto scanner at the baseline and then at the Avanto and Skyra scanners on the same day at the follow-up, on average 4.4 years (sd = 0.5 years) later. This allowed us to directly assess the effect of scanner and protocol change on the longitudinal change estimates. Eight subcortical brain regions were segmented using SAMSEG, and annualized symmetrized percent change in volume between time points was calculated. We find that RIDA significantly reduces between-scan effects and improves longitudinal volume estimates for the amygdala and lateral ventricles. It also reduces between-scan effects for caudate, putamen, and thalamus, but not as much as linear regression models. Whether the method will be useful for a particular study will depend on the image intensity profiles of the scans. Therefore, a pilot study of double-scanned participants is recommended to assess the advantages of the method for the analysis in question.
Investigating the eukaryotic host-like SLiMs in microbial mimitopes and their potential as novel drug targets for treating autoimmune diseases
Authors: Garg Anjali , Singhal Neelja , Kumar Manish 
Published: June 2022

AbstractSeveral pathogens sustain themselves inside the host by mimicking short linear motifs (SLiMs) of the host proteins. SLiMs are short stretches of 3-10 amino acids which are functionally diverse and mediate various signaling and protein-protein interactions (PPIs). Hence, mimicry of the host- SLiMs helps the microbes in modulating/disrupting the host defense mechanisms. This is the first report investigating the evolutionary characteristics and presence of eukaryotic host-like SLiMs in microbial peptides (mimitopes). Evaluation of the selection pressure revealed that 60% of the bacterial and 25% of the viral mimitopes which overlapped with the host-like SLiMs were evolutionarily conserved (ω < 1). Interestingly, host-like SLiMs were abundant in mimicry proteins but were less frequent in microbial mimitopes. This reflects that the majority of the pathogens cannot potentially rewire the host PPI networks for their advantage, but some can. Of the 152 bacterial and 43 viral mimitopes investigated only 10 bacterial and 4 viral mimitopes showed SLiMs. This indicates that mimitopes of some pathogens can be explored as novel drug targets for eliminating the etiopathological agent and treating the autoimmune disease, thereof. The repertoire of mimitopes identified here might provide important clues for the discovery of new drugs/protein-based immune-modulatory molecules against the pathogens.Key pointsMimicry of the host- SLiMs helps the microbes in modulating/disrupting the host defense mechanisms.Host-like SLiMs were abundant in mimicry proteins but were less frequent in microbial mimitopes.Evaluation of the selection pressure revealed that 60% of the bacterial and 25% of the viral mimitopes which overlapped with the host-like SLiMs were evolutionarily conserved.
Exchangeable HaloTag Ligands (xHTLs) for multi-modal super-resolution fluorescence microscopy
Authors: Kompa Julian , Bruins Jorick , Glogger Marius , Wilhelm Jonas , Frei Michelle S. , Tarnawski Miroslaw , D’Este Elisa , Heilemann Mike , Hiblot Julien , Johnsson Kai 
Published: June 2022

AbstractWe introduce exchangeable ligands for fluorescence labeling of HaloTag7 as an alternative to covalently bound probes. The exchangeable ligands open up new possibilities in imaging for a widely used labeling approach, including applications in points accumulation for imaging in nanoscale topography (PAINT), MINFLUX and live-cell, multi-frame stimulated emission depletion (STED) microscopy. We furthermore introduce orthogonal pairs of exchangeable ligands and HaloTags for dual-color PAINT and STED microscopy.Graphical Abstract
Epigenetic alterations in gut and brain of adult rats after oral administration of miR-320-3p and miR-375-3p at mid-lactation, and preventive potential of miR-320-3p on early weaning stress
Authors: Tavares Gabriel A , Torres Amada , Le Drean Gwenola , Queignec Maïwenn , Castellano Blandine , Tesson Laurent , Remy Séverine , Annegone Ignacio , de Souza Sandra L , Pitard Bruno , Kaeffer Bertrand 
Published: June 2022

AbstractAimTo investigate if the artificial delivery of microRNAs naturally present in the breastmilk can impact the gut and brain of young rats according to weaning.MethodsAnimals from a new transgenic rat line expressing green-fluorescent protein in the endocrine lineage (cholecystokinin expressing cells) received at Day-12, near neural diversification, a single oral bolus of mir-320-3p or miR-375-3p, embedded in DiOleyl-Succinyl-Paromomycin (DOSP), and were further early (Day-15) or regularly (Day-30) weaned. Relevant miRNA (miR-320-3p, miR-375-3p, miR-375-5p, miR-16-5p, miR-132-3p, miR-504), polr3d, hspb6, inflammation, enteroendocrine, and circadian clock-related mRNAs, chromatin complexes, and duodenal cell density were assayed at 8h post-inoculation and at Day-45.ResultsThe miR-320-3p/DOSP induced immediate effects on H3K4me3 chromatin complexes with polr3d promoter (p<0.05) but no long-term effects. On regular weaning, at Day-45, both miR-320-3p and 375-3p were down-regulated in the stomach, up-regulated in the hypothalamus (p<0.001) but only miR-320-3p was up-regulated in the duodenum. After early weaning, the miR-320-3p and miR-375-3p levels were down-regulated in the stomach and the duodenum, but up-regulated in the hypothalamus and the hippocampus. Combining miR-320-3p/DOSP with early weaning enhanced miR-320-3p and chromogranin A expression in the duodenum. In the hippocampus, the miR-504 was down-regulated for both sexes, but in the brain stem, up regulated only for females, along with miR-320-3p and miR-16-5p levels. In the hypothalamus, clock levels were up regulated for both sexes. In the miR-375-3p/DOSP group, the density of enteroendocrine duodenal cells increased. The long-term effect of miR-375-3p/DOSP was more limited, according to the fourfold lower number of predicted targets than with miR-320-3p.ConclusionAddressing oral miRNA-320-3p loads to duodenal cell lineage is paving the way for the design of new therapeutics, manipulating long term consequences of early life stress.
Differential coexistence of multiple genotypes ofOphiocordyceps sinensisin the stromata, ascocarps and ascospores of naturalCordyceps sinensis
Authors: Li Yu-Ling , Li Xiu-Zhang , Yao Yi-Sang , Wu Zi-Mei , Gao Ling , Tan Ning-Zhi , Luo Zhou-Qing , Xie Wei-Dong , Wu Jian-Yong , Zhu Jia-Shi 
Published: June 2022

AbstractObjectiveTo examine the differential occurrence ofOphiocordyceps sinensisgenotypes in the stroma, stromal fertile portion (SFP) densely covered with numerous ascocarps, and ascospores of naturalCordyceps sinensis.MethodsImmature and matureC. sinensisspecimens were harvested. MatureC. sinensisspecimens were continuously cultivated in our laboratory (altitude 2,200 m). The SFPs (with ascocarps) and ascospores ofC. sinensiswere collected for microscopic and molecular analyses using species-/genotype-specific primers. Sequences of mutant genotypes ofO. sinensiswere aligned with that of Genotype #1Hirsutella sinensisand compared phylogenetically using a Bayesian majority-rule method.ResultsFully and semiejected ascospores were collected from the same specimens. The semiejected ascospores tightly adhered to the surface of the asci as observed by the naked eye and under optical and confocal microscopies. The multicellular heterokaryotic ascospores showed uneven staining of nuclei. The immature and mature stromata, SFPs (with ascocarps) and ascospores were found to differentially contain several GC- and AT-biased genotypes ofO. sinensis, Samsoniella hepiali, and an AB067719-type fungus. The genotypes within AT-biased Cluster-A in the Bayesian tree occurred in all compartments ofC. sinensis, but those within AT-biased Cluster-B were present in immature and mature stromata and SPFs but absent in the ascospores. Genotype #13 ofO. sinensiswas present in semi-ejected ascospores and Genotype #14 in fully ejected ascospores. GC-biased Genotypes #13-14 featured large DNA segment substitutions and genetic material recombination between the genomes of the parental fungi (H. sinensisand the AB067719-type fungus). These ascosporic offspring genotypes combined with varying abundances ofS. hepialiin the 2 types of ascospores participated in the control of the development, maturation and ejection of the ascospores.ConclusionMultiple genotypes ofO. sinensiscoexist differentially in the stromata, SFPs and 2 types ofC. sinensisascospores, along withS. hepialiand the AB067719-type fungus. The fungal components in different combinations and their dynamic alterations in the compartments ofC. sinensisduring maturation play symbiotic roles in the lifecycle of naturalC. sinensis.
The cohesin subunit RAD21.2 functions as a recombination silencer of ribosomal DNA arrays
Authors: Kuttig Viola , Sims Jason , Hamamura Yuki , Komaki Shinichiro , Köhler Maren , Stolze Sara Christina , De Jaeger-Braet Joke , Tuncay Elbasy Hasibe , Nakagami Hirofumi , Failla Antonio Virgilio , Schlögelhofer Peter , Schnittger Arp 
Published: June 2022

Introductory ParagraphIn many species, including Arabidopsis, heterochromatin often comprises repetitive DNA elements, such as arrays of ribosomal DNA (rDNA). Repetitive regions pose a risk in meiosis since recombination between them can lead to gross genomic rearrangements. However, meiotic recombination at rDNA arrays and other heterochromatic repeat regions is blocked by not well understood mechanisms. Here, we have identified RAD21.2, an α-kleisin subunit of cohesin, as a repressor of meiotic recombination at the rDNA regions in Arabidopsis. We show that RAD21.2 co-localizes with heterochromatic factors and is specifically enriched at rDNA repeats, which are devoid of the meiosis specific α-kleisin REC8, needed for recombination. Knocking down RAD21.2, we find that REC8 moves into the nucleolus organizing regions (NORs), where we see an increase of RAD51 recombinase foci numbers. Concomitantly, we find extensive rearrangements of the NORs and the offspring of these plants have large variation in rDNA copy numbers demonstrating that RAD21.2 is necessary for transgenerational genome stability.One-Sentence SummaryThe cohesin component RAD21.2 represses meiotic recombination and by that contributes to genome stability over generations.
Novel strains of Campylobacter cause diarrheal outbreak in Rhesus macaques (Macaca mulatta) of Kathmandu Valley
Authors: Napit Rajindra , Manandhar Prajwol , Poudel Ajit , Rajbhandari Pragun G. , Watson Sarah , Shakya Sapana , Pradhan Saman M. , Sharma Ajay N. , Chaudhary Ashok , Johnson Christine K. , Mazet Jonna K. , Karmacharya Dibesh 
Published: June 2022

AbstractCampylobacter spp. is often underreported and underrated bacteria that present real health risks to both humans and animals, including non-human primates. It is a commensal microorganism of gastrointestinal tract known to cause gastroenteritis in humans. Commonly found in many wild animals including non-human primates (monkeys-Rhesus macaques) these pathogens are known to be a common cause of diarrhea in humans in many parts of developing and under developed countries.Rhesus macaques from the two holy sites in Kathmandu (Pashupati and Swoyambhu) were included in this cross-sectional study. Opportunistic diarrheal samples of monkeys were analyzed to detect and characterize the pathogen using 16S rRNA-based PCR screening, followed by DNA sequencing and phylogenetic analysis.Out of a total 67 collected diarrheal samples, Campylobacter spp. were detected in the majority of the samples (n=64; 96%). DNA sequences of the amplified PCR products were successfully obtained from 13 samples. Phylogenetic analysis identified Candidatus Campylobacter infans (n=10, Kimura-2 parameter (K2P) pairwise distance values of 0.002287). Remaining three sequences might potentially belong to a novel Campylobacter species/sub-species-closely relating to known species of C. helviticus (K2P pairwise distance of 0.0267). Both Candidatus Campylobacter infans and C. helvitucus are known to infect humans and animals. Additionally, we also detected the bacteria in water and soil samples from the sites. Campylobacter spp. caused the 2018 diarrhea outbreak in Rhesus macaques in the Kathmandu valley. Campylobacter might be one of the important contributing pathogens in diarrheal outbreaks-both in humans and animals (monkeys) in Nepal. Due to close interactions of these animals with humans and other animals, One Health approach might be the most effective way to prevent and mitigate the threat posed by this pathogen.
Oxygen concentration modulates colibactin production
Authors: Bossuet Nadège , Guyonnet Cécile , Chagneau Camille V , Tang-Fichaux Min , Penary Marie , Loubet Dorian , Branchu Priscilla , Oswald Eric , Nougayrede Jean-Philippe 
Published: June 2022

AbstractUp to 25% of theE. colistrains isolated from the feces of healthy humans harbor thepksgenomic island encoding the synthesis of colibactin, a genotoxic metabolite. Evidence is accumulating for an etiologic role of colibactin in colorectal cancer. Little is known about the conditions of expression of colibactin in the gut. The intestine is characterized by a unique oxygenation profile, with a steep gradient between the physiological hypoxic epithelial surface and the anaerobic lumen, which favors the dominance of obligate anaerobes. Here, we report that colibactin production is maximal under anoxic conditions and decreases with increased oxygen concentration. We show that the aerobic respiration control (ArcA) positively regulates colibactin production and genotoxicity ofpks+ E. coliin response to oxygen availability. Thus, colibactin synthesis is inhibited by oxygen, indicating that thepksbiosynthetic pathway is adapted to the anoxic intestinal lumen and to the hypoxic infected or tumor tissue.
Financial inclusion using corporate social responsibility: a socio-economic demand–supply analysis
Authors: Ibne Afzal Munshi Naser , Nayeem Sadi Md Abu , Siddiqui Shamim Ahmad 
Published: June 2022

PurposeCorporate social responsibility (CSR) aims at upholding socio-economic condition of deprived communities prevailing in society as well as bringing profitability for corporate companies themselves. This study investigates to what extent the CSR initiatives of financial institutions in Bangladesh have been able to reach out to deprived communities and support various dimensions of financial inclusion (FI) in the country.Design/methodology/approachIn this study, both supply-side and demand-side data are included and discussed rigorously as tools to cross-check the result. Both qualitative and quantitative data are incorporated, and graphs and tables are used to represent the critical information better. A triangulation of in-depth interviews with secondary data is used to ensure rigor and trustworthiness. The triangulation approach works as a method to verify secondary data by interviewees in this study.FindingsThe result shows a positive geographical and demographical penetration of CSR activities, but it does not necessarily bring FI in all cases. This study identifies some key issues that prevail in the current context of Bangladesh, such as usage, distance, quality and cost of financial products.Originality/valueThis study makes use of both supply-side and demand-side information and thus explain the reasons behind the involuntary exclusion of financial services.