bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life
Authors: Méheust Raphaël , Huang Shuo , Rivera-Lugo Rafael , Banfield Jillian F. , Light Samuel H. 
Published: January 2021

AbstractDisparate redox activities that take place beyond the bounds of the prokaryotic cell cytosol must connect to membrane or cytosolic electron pools. Proteins post-translationally flavinylated by the enzyme ApbE mediate electron transfer in several characterized extracytosolic redox systems but the breadth of functions of this modification remains unknown. Here we present a comprehensive bioinformatic analysis of 31,910 prokaryotic genomes that provides evidence of extracytosolic ApbEs within ~50% of bacteria and the involvement of flavinylation in numerous uncharacterized biochemical processes. By mining flavinylation-associated gene clusters, we identify five protein classes responsible for transmembrane electron transfer and two domains of unknown function (DUF2271 and DUF3570) that are flavinylated by ApbE. We observe flavinylation/iron transporter gene colocalization patterns that implicate functions in iron reduction and assimilation. We find associations with characterized and uncharacterized respiratory oxidoreductases that highlight roles of flavinylation in respiratory electron transport chains. Finally, we identify interspecies gene cluster variability consistent with flavinylation/cytochrome functional redundancies and discover a class of “multi-flavinylated proteins'' that may resemble multiheme cytochromes in facilitating longer distance electron transfer. These findings provide key mechanistic insight into an important facet of bacterial physiology and establish flavinylation as a functionally diverse mediator of extracytosolic electron transfer.Impact StatementBioinformatic and biochemical studies find that covalently bound flavins are common and participate in wide-ranging extracytosolic redox activities throughout bacterial life.
International risk of the new variant COVID-19 importations originating in the United Kingdom
Authors: Du Zhanwei , Wang Lin , Yang Bingyi , Ali Sheikh Taslim , Tsang Tim K. , Shan Songwei , Wu Peng , Lau Eric H. Y. , Cowling Benjamin J. , Meyers Lauren Ancel 
Published: January 2021

AbstractA fast-spreading SARS-CoV-2 variant identified in the United Kingdom in December 2020 has raised international alarm. We estimate that, in all 15 countries analyzed, there is at least a 50% chance the variant was imported by travelers from the United Kingdom by December 7th.
Exo-β-N-acetylmuramidase NamZ ofBacillus subtilisis the founding member of a family of exo-lytic peptidoglycan hexosaminidases
Authors: Müller Maraike , Calvert Matthew , Hottmann Isabel , Kluj Robert Maria , Teufel Tim , Balbuchta Katja , Engelbrecht Alicia , Selim Khaled A. , Xu Qingping , Borisova Marina , Titz Alexander , Mayer Christoph 
Published: January 2021

ABSTRACTEndo-β-N-acetylmuramidases, commonly known as lysozymes, are well-characterized antimicrobial enzymes that potentially lyse bacterial cells. They catalyze an endo-lytic cleavage of the peptidoglycan, the structural component of the bacterial cell wall; i.e. they hydrolyze glycosidicN-acetylmuramic acid (MurNAc)-β-1,4-N-acetylglucosamine (GlcNAc)-bonds within the heteroglycan backbone of peptidoglycan. In contrast, little is known about exo-β-N-acetylmuramidases, catalyzing an exo-lytic cleavage of β-1,4-MurNAc entities from the non-reducing ends of peptidoglycan chains. Such an enzyme was identified earlier in the bacteriumBacillus subtilis, but the corresponding gene has remained unknown so far. We identifiedybbCofB. subtilis,renamednamZ, as encoding the reported exo-β-N-acetylmuramidase. A ΔnamZmutant accumulated specific cell wall fragments and showed growth defects under starvation conditions, indicating a role of NamZ in cell wall turnover. Recombinant NamZ protein specifically hydrolyzed the artificial substrate para-nitrophenyl β-MurNAc and the peptidoglycan-derived disaccharide MurNAc-β-1,4-GlcNAc. Together with the exo-β-N-acetylglucosaminidase NagZ and the exo-muramoyl-L-alanine amidase AmiE, NamZ degraded intact peptidoglycan by sequential hydrolysis from the non-reducing ends. NamZ is a member of the DUF1343 protein family of unknown function and shows no significant sequence identity with known glycosidases. A structural model of NamZ revealed a putative active site located in a cleft within the interface of two subdomains, one of which constituting a Rossmann-fold-like domain, unusual for glycosidases. On this basis, we propose that NamZ represents the founding member of a novel family of peptidoglycan hexosaminidases, which is mainly present in the phylum Bacteroidetes and, less frequently, within Firmicutes (Bacilli, Clostridia), Actinobacteria and Gammaproteobacteria.
Comparative genomic analysis and characterization ofStaphylococcussp. AOAB, isolated from a notoriously invasiveMnemiopsis leidyigut revealed multiple antibiotic resistance determinants
Authors: Mariita Richard M. , Hossain Mohammad J. , Moss Anthony G. 
Published: January 2021

AbstractHere, we describe the isolation and characterization of a coagulase-negative, vancomycin and oxacillin-susceptible novel bacterium of the genusStaphylococcus. Staphylococcussp. strain AOAB was isolated from the stomodeum (gut) of theMnemiopsis leidyifrom Mobile Bay, Alabama USA. A polyphasic taxonomic approach comprised of phenotypic, chemotaxonomic and genotypic characteristics was used for analysis. The dominant respiratory quinone detected was MK-7 (100%). Major cellular fatty acids were anteiso-C15:0(40.52%), anteiso-C17:0(13.04 %), C-18:0(11.53%) and C-20:0(10.45%). The polar lipid profile consisted of glycolipid, phospholipid, phosphatidylglycerol and diphosphatidylglycerol. Although strain AOAB had a 16SrRNA gene sequence similarity of 99% withS. warneriSG1,S. pasteuri, S. devrieseiKS-SP_60,S. lugdunensisHKU09-01,S. epidermidisRP62A,S. haemolyticusJCSC1435 andS. hominisDM 122, it was be distinguished from those species based on Multi-Locus Sequence Analysis (MLSA) using 6 marker genes (16S rRNA,hsp60, rpoB, dnaJ, sodAandtuf). MLSA revealed strain AOAB to be closely related toS. warneriSG1 andS. pasteuriSP1 but distinct from two hitherto known species. These results were confirmed by Average Nucleotide Identity (closest ANI of 84.93% and 84.58% identity againstS. warneriSG1 andS. pasteuriSP1 respectively).In-silicoDNA-DNA hybridization was <70% (33.1 % and 32.8% againstS. warneriSG1 andS. pasteuriSP1 respectively), which further confirmed that the strain was a potential novelStaphylococcusspecies.
Mapping the Promiscuous Binding Interface of HOX-A11 with KIX by Experimentally Guidedin-silicodocking
Authors: Ganguly Soumya , Wagner Günter P. , Meiler Jens 
Published: January 2021

AbstractTranscription factors (TFs) regulate levels of transcription through a complex array of protein-protein interactions, thereby controlling key physiological processes such as development, stress response and cell growth. The transcription factor HOXA11 contains an intrinsically disordered regions (IDR) through which it interacts with CREB binding protein (CBP) and regulates endometrial development and function in eutherian mammals. The interaction between the IDR of HOXA11 and CBP was analyzed using computational docking guided by experimental constraints. HOXA11 IDR interacts with the KIX domain of CBP at two discrete sites – MLL and cMyb, mediated by sticky hydrophobic grooves on the surface of KIX. A five residue motif FDQFF on HOXA11 can interact both at cMyb and MLL site of KIX resulting in a promiscuous binding.Author SummaryWe demonstrate how the intrinsically disordered region (IDR) of transcription factor HOXA11 interacts at two distinct sites of the transcription coactivator CREB binding protein (CBP). By combining computational docking with limited experimental data we construct models of the complex of the KIX domain within CBP and a short helical segment within the IDR of HOXA11. The interaction between HOXA11 and CBP is believed to trigger the downstream expression of genes important in embryonic development.
Complex phyllosphere microbiome aids in the establishment of the invasive macrophyteHydrilla verticillata(L.) under conditions of nitrogen scarcity
Authors: Bárta Jiří , de Paula Caio Cesar Pires , Rejmánková Eliška , Lin Qiang , Kohoutová Iva , Sirová Dagmara 
Published: January 2021

AbstractDespite the low availability of nitrogen (N), the highly productive macrophyteHydrilla verticillata(L.) is a successful invader of the littoral zones at lake Atitlán, Guatemala, with profound implications for lake ecology. To help answer the question of howHydrilla, accompanied by the filamentous green algaCladophoraKützing (Ulvophyceae), sustains fast growth under conditions of N scarcity, we studied the composition and potential biogeochemical function of the associated microbiomes. We combined results from next generation sequencing of associated bacterial and fungal assemblages with traditional microscopy-based taxonomical evaluation of algae and cyanobacteria. We focused on the presence of specific N2-fixing genera and their relative importance. Data on community composition are complemented with measurements of diazotrophic activity. The results expand our knowledge of the ecophysiology of these algae-plant-microbe consortia and suggest that several levels of biological complexity should be considered to fully understand aquatic plant ecology and the process of macrophyte invasions.
Dissecting lipid contents in the distinct regions of native retinal rod disk membranes
Authors: Sander Christopher L. , Sears Avery E. , Pinto Antonio F. M. , Choi Elliot H. , Kahremany Shirin , Jin Hui , Pardon Els , Suh Susie , Dong Zhiqian , Steyaert Jan , Saghatelian Alan , Skowronska-Krawczyk Dorota , Kiser Philip D. , Palczewski Krzysztof 
Published: January 2021

ABSTRACTPhotoreceptors rely on distinct membrane compartments to support their specialized function. Unlike protein localization, identification of critical differences in membrane content has not yet been expanded to lipids, due to the difficulty of isolating domain-specific samples. We have overcome this by using SMA to co-immunopurify membrane proteins and their native lipids from two regions of photoreceptor ROS disks. Each sample’s copurified lipids were subjected to untargeted lipidomic and fatty acid analysis. Extensive differences between center (rhodopsin) and rim (ABCA4 and PRPH2/ROM1) samples included a lower PC to PE ratio and increased LC- and VLC-PUFAs in the center relative to the rim region, which were enriched in shorter, saturated FAs. The comparatively few differences between the two rim samples likely reflect specific protein-lipid interactions. High-resolution profiling of the ROS disk lipid composition provides a model for future studies of other complex cellular structures, and gives new insights into how intricate membrane structure and protein activity are balanced within the ROS.SUMMARYSander et al. have parsed the lipid composition of native-source photoreceptor disks and find large differences in fatty acid unsaturation and chain length between the center and rim regions. They selectively copurify membrane proteins and lipids from each region in SMALPs using nanobodies and antibodies.
High levels of Dorsal transcription factor downregulate, not promote,snailexpression by regulating enhancer action
Authors: Irizarry Jihyun , McGehee James , Stathopoulos Angelike 
Published: January 2021

AbstractInDrosophilaembryos, genes expressed along the dorsal-ventral axis are responsive to concentration of the Dorsal (Dl) transcription factor, which varies in space; however, levels of this morphogen also build over time. Since expression of high-threshold Dl target genes such assnail(sna) is supported before Dl levels peak, it is unclear what role increasing levels have if any. Here we investigated action of two enhancers that controlsnaexpression in embryos, demonstrating using genome editing that Dl binding sites within one enhancer located promoter proximally,sna.prox, can limit the ability of the other distally-located enhancer,sna.dis, to increasesnalevels. In addition, MS2-MCP live imaging was used to studysnatranscription rate in wildtype,dlheterozygote, and a background in which a photo-sensitive degron is fused to Dl (dl-BLID). The results demonstrate that, when Dl levels are high, Dl acts throughsna.proxto limit the activity ofsna.disand thereby influencesnatranscription rate. In contrast, when Dl levels are kept low usingdl-BLID, sna.proxpositively influencessnatranscription rate. Collectively, our data support the view that Dl’s effect on gene expression changes over time, switching from promotingsnaexpression at low concentration to dampeningsnaexpression at high concentration by regulating enhancer interactions. We propose this differential action of the Dl morphogen is likely supported by occupancy of this factor first to high and then low affinity binding sites over time as Dl levels rise to coordinate action of these two co-acting enhancers.Significance statementA gradient of the maternal transcription factor Dorsal is important for establishing spatial expression of target genes along the dorsal-ventral axis ofDrosophilaembryos. Dorsal levels are also dynamic as nuclear concentration builds in time. Surprisingly, expression of high-threshold target genes such assnailis supported before levels peak, raising the question why levels continue to build. Our data support the view that peak Dorsal levels act to preferentially support activity of one enhancer over another to effectively decreasesnailexpression. In addition, while the morphogen Dorsal acts early to support gene expression, later it effectively acts as a damper to limit gene expression. Our results suggest other morphogens also have effects on gene expression that change over time.
Evolving cryo-EM structural approaches for GPCR drug discovery
Authors: Zhang Xin , Johnson Rachel M. , Drulyte Ieva , Yu Lingbo , Kotecha Abhay , Danev Radostin , Wootten Denise , Sexton Patrick M. , Belousoff Matthew J. 
Published: January 2021

AbstractG protein-coupled receptors (GPCRs) are the largest class of cell surface drug targets. Advances in biochemical approaches for the stabilisation of GPCR:transducer complexes together with improvements in the technology and application of cryo-EM has recently opened up new possibilities for structure-assisted drug design of GPCR agonists. Nonetheless, limitations in the commercial application of some of these approaches, including the use of nanobody 35 (Nb35) for stabilisation of GPCR:Gs complexes, and the high cost of 300kV imaging have restricted broad application of cryo-EM in drug discovery. Here, using the PF 06882961-bound GLP-1R as exemplar, we validated formation of stable complexes with a modified Gs protein in the absence of Nb35 that had equivalent resolution in the drug binding pocket to complexes solved in the presence of Nb35, while the G protein displayed increased conformational dynamics. In parallel, we assessed the performance of 200kV versus 300kV image acquisition using a Falcon 4 or K3 direct electron detector. We show that with 300kV Krios, both bottom mounted Falcon 4 and energy filtered (25eV slit) Bio-Quantum K3 produced similar resolution. Moreover, the 200kV Glacios with bottom mounted Falcon 4 yielded a 3.2 Å map with clear density for bound drug and multiple structurally ordered waters. Our work paves the way for broader commercial application of cryo-EM for GPCR drug discovery.
Cooperative Communication with Humans Evolved to Emerge Early in Dogs
Authors: Salomons Hannah , Smith Kyle , Callahan-Beckel Megan , Callahan Margaret , Levy Kerinne , Kennedy Brenda S. , Bray Emily , Gnanadesikan Gitanjali E. , Horschler Daniel J. , Gruen Margaret , Tan Jingzhi , White Philip , MacLean Evan , Hare Brian 
Published: January 2021

AbstractWhile we know that dogs evolved from wolves through a process of domestication, it remains unclear how this process may have affected dog cognitive development. Here we tested dog (N=44) and wolf (N=37) puppies, 5-18 weeks old, on a battery of temperament and cognition tasks. Dog puppies were more attracted to humans, read human gestures more skillfully and made more eye contact with humans than wolf puppies. The two species were similarly attracted to objects and performed similarly on nonsocial measures of memory and inhibitory control. These results demonstrate the role of domestication in enhancing the cooperative communication skills of dogs through selection on attraction to humans, which altered developmental pathways.One Sentence SummaryDomestication altered dogs’ developmental pathways to enhance their cooperative communication with humans.
Nucleus accumbens neurons encode initiation and vigor of reward approach behavior
Authors: Levcik David , Sugi Adam H. , Pochapski José A. , Baltazar Gabriel , Pulido Laura N. , Villas-Boas Cyrus , Aguilar-Rivera Marcelo , Fuentes-Flores Romulo , Nicola Saleem M. , Cunha Claudio Da 
Published: January 2021

AbstractThe nucleus accumbens (NAc) is considered an interface between motivation and action, with NAc neurons playing an important role in promoting reward approach. However, the encoding by NAc neurons that contribute to this role remains unknown. Here, we trained male rats to find rewards in an 8-arm radial maze. The activity of 62 neurons, mostly in the shell of the NAc, were recorded while rats ran towards each reward place. General linear model (GLM) analysis showed that variables related to the vigor of the locomotor approach, like speed and acceleration, and the fraction of the approach run completed were the best predictors of the firing rate for most NAc neurons. Nearly 23% of the recorded neurons, here named locomotion-off cells, were inhibited during the entire approach run, suggesting that reduction in firing of these neurons promotes initiation of locomotor approach. Another 24% of the neurons presented a peak of activity during acceleration followed by a valley during deceleration (peak-valley cells). Together, these neurons accounted for most of the speed and acceleration encoding identified in the GLM analysis. Cross-correlations between firing and speed indicated that the spikes of peak-valley cells were followed by increases in speed, suggesting that the activity of these neurons drives acceleration. In contrast, a further 19% of neurons presented a valley during acceleration followed by a peak just prior to or after reaching reward (valley-peak cells). These findings suggest that these three classes of NAc neurons control the initiation and vigor of the locomotor approach to reward.Significance StatementDeciphering the mechanisms by which the NAc controls the vigor of motivated behavior is critical to better understand and treat psychiatric conditions in which motivation is dysregulated. Manipulations of the NAc profoundly impair subjects’ ability to spontaneously approach reward-associated locations, preventing them from exerting effort to obtain reward. Here, we identify for the first time specific activity of NAc neurons in relation to spontaneous approach behavior. We discover three classes of neurons that could control initiation of movement and the speed vs. time trajectory during locomotor approach. These results suggest a prominent but heretofore unknown role for the NAc in regulating the kinematics of reward approach locomotion.
Novel RT-ddPCR Assays for determining the transcriptional profile of SARS-CoV-2
Authors: Telwatte Sushama , Kumar Nitasha , Vallejo-Gracia Albert , Kumar G. Renuka , Lu Chuanyi M. , Ott Melanie , Wong Joseph K. , Yukl Steven A. 
Published: January 2021

AbstractThe exact mechanism of coronavirus replication and transcription is not fully understood; however, a hallmark of coronavirus transcription is the generation of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and an array of subgenomic mRNAs (sgRNAs) encompassing sequences arising from discontinuous transcription.Existing PCR-based diagnostic assays for SAR-CoV-2 are qualitative or semi-quantitative and do not provide the resolution needed to assess the complex transcription dynamics of SARS-CoV-2 over the course of infection. We developed and validated a novel panel of specially designed SARS-CoV-2 ddPCR-based assays to map the viral transcription profile. Application of these assays to clinically relevant samples will enhance our understanding of SARS-CoV-2 replication and transcription and may also inform the development of improved diagnostic tools and therapeutics.HighlightsWe developed a novel panel of 7 quantitative RT-ddPCRs assays for SARS-Cov-2Our panel targets nongenic and genic regions in genomic and subgenomic RNAsAll assays detect 1-10 copies and are linear over 3-4 orders of magnitudeAll assays correlated with the clinical Abbott SARS-CoV-2 Viral Load AssayClinical samples showed higher copy numbers for targets at the 3’ end of the genome
MR relaxometry-based analysis of brain hemorrhages: an experimental study on a rabbit model
Authors: Del Signore Francesca , Vignoli Massimo , Salda Leonardo Della , Tamburro Roberto , Cerasoli Ilaria , Paolini Andrea , Romanucci Mariarita , de Pasquale Francesco 
Published: January 2021

AbstractMagnetic Resonance Relaxometry is a quantitative MRI-based technique able to estimate tissue relaxation times T1 and T2. This approach allows increasing the MRI diagnostic accuracy mostly in case of brain neoplasia or neurodegenerative disorders in human medicine. However, few reports are available on the application of this technique in the clinical field of veterinary medicine. For this reason, in this work, we developed a relaxometry based approach on experimentally induced brain hemorrhages on rabbits. Specifically, the methodology is based on a hierarchical clustering procedure driven by the T1 relaxometry signals from a set of regions of interest selected on the T2 map. The approach is multivariate since it combines both T1 and T2 information and allows the diagnosis at the subject level by comparing “suspected” pathological regions with healthy homologous ones within the same brain.To validate the proposed technique, the scanned brains underwent histopathological analyses to estimate the performance of the proposed classifier in terms of Receiver Operator Curve analyses. The results showed that, in terms of identification of the lesion and its contours, the proposed approach resulted accurate and outperformed the standard techniques based on T1w and T2w images. Finally, since the proposed protocol in terms of the adopted scanner, sequences, and analysis tools, is suitable for the clinical practice, it can be potentially validated through large-scale multi-center clinical studies.