bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of N-Glycan Outer Chain like α-(1→6)-linked Mannan Structures inAspergillus fumigatusMycelium
Authors: Kadooka Chihiro , Tanaka Yutaka , Kishida Rintaro , Hira Daisuke , Oka Takuji 
Published: December 2023

AbstractThe cellular surface of the pathogenic filamentous fungusAspergillus fumigatusis enveloped in a mannose layer, featuring well-established fungal-type galactomannan and O-mannose type galactomannan. This study reports the discovery of cell wall component in the mycelium that resemble N-glycan outer chains found in yeast. The glycosyltransferases involved in their biosynthesis inA. fumigatuswere identified, with a focus on two key α-(1→2)-mannosyltransferases, Mnn2 and Mnn5, and two crucial α-(1→6)-mannosyltransferases, Mnn9 and Van1.In vitroexamination revealed the roles of Mnn2 and Mnn5 in transferring α-(1→2)-mannosyl residues.1H-NMR analysis of cell wall extracts from the Δmnn2Δmnn5strain indicated the existence of an α-(1→6)-linked mannan backbone in the mycelium, with Mnn2 and Mnn5 adding α-(1→2)-mannosyl residues to this backbone. The α-(1→6)-linked mannan-derived chemical shift was absent in strains wheremnn9orvan1was disrupted in the parental Δmnn2Δmnn5strain. Co-expressed Mnn9 and Van1 functioned as α-(1→6)-linked mannan polymerases in heterodimers, suggesting their crucial role in biosynthesizing the α-(1→6)-linked mannan backbone. Disruptions in these mannosyltransferases did not affect fungal-type galactomannan biosynthesis. The study provides insights into the complexity of fungal cell wall architecture and a comprehensive understanding of mannan biosynthesis inA. fumigatus,including the presence of outer chain like mannan structures and their potential role in cell wall integrity.ImportanceThis study unravels the complexities of mannan biosynthesis inA. fumigatus,a key area for antifungal drug discovery. It reveals the presence of outer chain like mannan structures, offering fresh insights into the fungal cell wall’s design. Key enzymes Mnn2, Mnn5, Mnn9, and Van1 are instrumental in this process, with Mnn2 and Mnn5 adding specific mannose residues and Mnn9 and Van1 assembling the outer chain like structures. While fungal-type galactomannan’spresence in the cell wall is known, the existence of outer chain like mannan adds a new dimension to our understanding. This intricate web of mannan biosynthesis opens avenues for further exploration and enhances our understanding of fungal cell wall dynamics, paving the way for targeted drug development.
Electrostatic encoding of genome organization principles within single native nucleosomes
Authors: Park Sangwoo , Athreya Advait , Carrizo Gustavo Ezequiel , Benning Nils A. , Mitchener Michelle M. , Bhanu Natarajan V. , Garcia Benjamin A. , Zhang Bin , Muir Tom W. , Pearce Erika L. , Ha Taekjip 
Published: December 2023

ABSTRACTThe eukaryotic genome, first packed into nucleosomes of about 150 bp around the histone core, is organized into euchromatin and heterochromatin, corresponding to the A and B compartments, respectively. Here, we asked if individual nucleosomes in vivo know where to go. That is, do mono-nucleosomes by themselves contain A/B compartment information, associated with transcription activity, in their biophysical properties? We purified native mono-nucleosomes to high monodispersity and used physiological concentrations of biological polyamines to determine their condensability. The chromosomal regions known to partition into A compartments have low condensability and vice versa.In silicochromatin polymer simulations using condensability as the only input showed that biophysical information needed to form compartments is all contained in single native nucleosomes and no other factors are needed. Condensability is also strongly anticorrelated with gene expression, and especially so near the promoter region and in a cell type dependent manner. Therefore, individual nucleosomes in the promoter know whether the gene is on or off, and that information is contained in their biophysical properties. Comparison with genetic and epigenetic features suggest that nucleosome condensability is a very meaningful axis onto which to project the high dimensional cellular chromatin state. Analysis of condensability using various condensing agents including those that are protein-based suggests that genome organization principle encoded into individual nucleosomes is electrostatic in nature. Polyamine depletion in mouse T cells, by either knocking out ornithine decarboxylase (ODC) or inhibiting ODC, results in hyperpolarized condensability, suggesting that when cells cannot rely on polyamines to translate biophysical properties of nucleosomes to control gene expression and 3D genome organization, they accentuate condensability contrast, which may explain dysfunction known to occur with polyamine deficiency.
Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information
Authors: Xu Da , Ando Nozomi 
Published: December 2023

AbstractEfficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models that have been proven successful in many computer vision tasks, and have been previously applied to cryo-EM micrograph filtering. In this work, we demonstrate that two strategies, fine-tuning models from pretrained weights and including the power spectrum of micrographs as input, can greatly improve the attainable prediction accuracy of CNN models. The resulting software package, Miffi, is open-source and freely available for public use (https://github.com/ando-lab/miffi).
Environmental gradients mediate dispersal evolution during biological invasions
Authors: Benning John W. , Clark Eliza I. , Hufbauer Ruth A. , Weiss-Lehman Christopher 
Published: December 2023

AbstractRapid dispersal evolution at the edge of a range expansion can accelerate invasions. However, expanding populations will often encounter environmental gradients that entail a fitness cost of dispersal. We used an eco-evolutionary model to explore how environmental heterogeneity influences adaptation and dispersal evolution during range expansion and, in turn, modulates the speed and predictability of invasion. Environmental gradients opposed the evolution of increased dispersal during invasion, even leading to the evolution of reduced dispersal along steep gradients. Counterintuitively, reduced dispersal allowed for faster expansion by minimizing maladaptation. While evolution across homogenous landscapes caused invasions to be highly unpredictable, even shallow environmental gradients greatly increased invasion predictability. We illustrate our model’s potential application to prediction and management of invasions by parameterizing it with data from a recent invertebrate range expansion. Overall, we find that environmental heterogeneity and local adaptation strongly modulate the effect of dispersal evolution on invasion trajectories.
Elucidating the activation mechanism of the proton-sensing GPR68 receptor
Authors: Matsingos Christos , Howell Lesley A. , McCormick Peter J. , Fornili Arianna 
Published: December 2023

ABSTRACTGPR68 is a proton-sensing G-protein Coupled Receptor (GPCR) involved in a variety of physiological processes and disorders including neoplastic pathologies. While GPR68 and few other GPCRs have been shown to be activated by a decrease in the extracellular pH, the molecular mechanism of their activation remains largely unknown. In this work, we used a combined computational andin vitroapproach to provide new insight into the activation mechanism of the receptor. Molecular Dynamics simulations of GPR68 were used to model the changes in residue interactions and motions triggered by pH. Global and local rearrangements consistent with partial activation were observed upon protonation of the inactive state. Selected extracellular histidine and transmembrane acidic residues were found to have significantly upshifted pKavalues during the simulations, consistently with their previously hypothesised role in activation through changes in protonation state. Moreover, a novel pairing between histidine and acidic residues in the extracellular region was highlighted by both sequence analyses and simulation data and tested through site-directed mutagenesis. At last, we identified a previously unknown hydrophobic lock in the extracellular region that might stabilise the inactive conformation and regulate the transition to the active state.g
IgDesign:In vitrovalidated antibody design against multiple therapeutic antigens using inverse folding
Authors: Shanehsazzadeh Amir , Alverio Julian , Kasun George , Levine Simon , Calman Ido , Khan Jibran A. , Chung Chelsea , Diaz Nicolas , Luton Breanna K. , Tarter Ysis , McCloskey Cailen , Bateman Katherine B. , Carter Hayley , Chapman Dalton , Consbruck Rebecca , Jaeger Alec , Kohnert Christa , Kopec-Belliveau Gaelin , Sutton John M. , Guo Zheyuan , Canales Gustavo , Ejan Kai , Marsh Emily , Ruelos Alyssa , Ripley Rylee , Stoddard Brooke , Caguiat Rodante , Chapman Kyra , Saunders Matthew , Sharp Jared , da Silva Douglas Ganini , Feltner Audree , Ripley Jake , Bryant Megan E. , Castillo Danni , Meier Joshua , Stegmann Christian M. , Moran Katherine , Lemke Christine , Abdulhaqq Shaheed , Klug Lillian R. , Bachas Sharrol 
Published: December 2023

AbstractDeep learning approaches have demonstrated the ability to design protein sequences given backbone structures [1, 2, 3, 4, 5]. While these approaches have been appliedin silicoto designing antibody complementarity-determining regions (CDRs), they have yet to be validatedin vitrofor designing antibody binders, which is the true measure of success for antibody design. Here we describeIgDesign, a deep learning method for antibody CDR design, and demonstrate its robustness with successful binder design for 8 therapeutic antigens. The model is tasked with designing heavy chain CDR3 (HCDR3) or all three heavy chain CDRs (HCDR123) using native backbone structures of antibody-antigen complexes, along with the antigen and antibody framework (FWR) sequences as context. For each of the 8 antigens, we design 100 HCDR3s and 100 HCDR123s, scaffold them into the native antibody’s variable region, and screen them for binding against the antigen using surface plasmon resonance (SPR). As a baseline, we screen 100 HCDR3s taken from the model’s training set and paired with the native HCDR1 and HCDR2. We observe that both HCDR3 design and HCDR123 design outperform this HCDR3-only baseline. IgDesign is the first experimentally validated antibody inverse folding model. It can design antibody binders to multiple therapeutic antigens with high success rates and, in some cases, improved affinities over clinically validated reference antibodies. Antibody inverse folding has applications to bothde novoantibody design and lead optimization, making IgDesign a valuable tool for accelerating drug development and enabling therapeutic design. The data generated in this study serve as a useful benchmark of diverse antibody-antigen interactions. We use this data to benchmark self-consistency RMSD (scRMSD), using ABodyBuilder2 [6], ABodyBuilder3 [7], and ESMFold [8], as a metric for assessing binding. We open source the code for IgDesign and the SPR datasets.Code and datasets can be found athttps://github.com/AbSciBio/igdesign.
Medical students’ perceptions towards artificial intelligence in education and practice: A multinational, multicenter cross-sectional study
Authors: Busch Felix , Hoffmann Lena , Truhn Daniel , Ortiz-Prado Esteban , Makowski Marcus R. , Bressem Keno K. , Adams Lisa C. 
Published: December 2023

AbstractBackgroundArtificial intelligence (AI) is anticipated to fundamentally change the educational and professional landscape for the next generation of physicians, but its successful integration depends on the global perspectives of all stakeholders. Previous medical student surveys were limited by small sample sizes or geographic constraints, hindering a global comparison of perceptions. This study aims to explore current medical students’ attitudes towards AI in medical education and the profession on a broad, international scale and to examine regional differences in perspectives.Methods and FindingsThis international multicenter cross-sectional study developed and validated an anonymous online survey of 15 multiple-choice items to assess medical, dentistry, and veterinary students’ AI knowledge and attitudes toward the utilization of AI in healthcare, the current state of AI education, and regional differences in perspectives. Between April and October 2023, 4,313 medical, 205 dentistry, and 78 veterinary students from 192 faculties in 48 countries responded to the survey (average response rate: 0.2%, standard deviation: 0.4%). Most participants studied in European countries (N=2,350), followed by North/South America (N=1,070) and Asia (N=944). Students expressed predominantly positive attitudes towards the use of AI in healthcare (67.6%, N=3,091) and the desire for more AI teaching in their curricula (76.1%, N=3,474). However, they reported limited general knowledge of AI (75.3%, N=3,451), the absence of AI-related courses (76.3%, N=3,497), and felt inadequately prepared to use AI in their future careers (57.9%, N=2,652). The subgroup analyses revealed regional differences in perceptions, although predominantly with small effect sizes. The main limitations include the low response rate per institution, which was calculated on total enrollment across all degree programs, and the risk of selection bias.ConclusionsThis study highlights the favorable perceptions of international medical students towards incorporating AI in healthcare practice while emphasizing the importance of integrating AI teaching into medical education.Graphical abstract
Skin microbiota variation in Indian families
Authors: Potbhare Renuka , Ravikumar Ameeta , Munukka Eveliina , Ashma Richa , Lahti Leo 
Published: December 2023

AbstractBackgroundIn Indian culture, extended families have symbolized our tradition. Families often encompass members spanning multiple generations cohabiting the same household, thereby sharing ethnicity, genetics, dietary habits, lifestyles, and living conditions. The joint or extended family setup provides an opportunity to compare variations in microbiota composition within and between families. While previous research has demonstrated that skin microbiota can be influenced by factors such as ethnicity, geography, diet, age, and sex, its associations among Indian family members that may share also genetic background remains largely unexplored.MethodsThe present study involved seventy-two individuals from fifteen families in two geographical regions of Maharashtra, India. Bacterial DNA was extracted from axillary sweat samples, followed by sequencing of V3-V4 regions of the 16S rRNA. The generated taxonomic profiles were used to quantify microbiota diversity and similarities in skin microbiota composition within and between families, taking into account factors such as genetic relatedness, diet, sex, age, geographical location, and co-habitation.ResultsThe skin microbiota composition typically comprised Firmicutes, Proteobacteria, and Actinobacteria phyla. Notably, the Shannon alpha diversity was moderately associated with dietary habits and geographical location (Kruskal-Wallis; FDR<0.1), whereas no significant differences were observed for other key factors such as age, location, or sex. A significant association was also observed between taxonomic composition and shared familial membership (p=0.001; PERMANOVA), with a borderline significant association with geographical location (p=0.07). When within and between family comparisons were investigated across three generation (G1-G2, G2-G3 and G1-G3), no significant differences were observed, however, in general skin microbiota was more similar within than between families.ConclusionThis study underscores the diversity and commonalities in skin microbiota composition within and between families. We observed that every family has a unique skin microbiota and among the various covariates, significant association was observed for diet and geographical location. Our study highlights that family relations may have specific associations with skin microbiota composition and diversity. Further studies with larger sample sizes will help to elucidate the relative contributions of shared co-habitation and genetic backgrounds.
Structural insights into specific recognition of PTENα/β-NTE by WDR5 in cancer progression
Authors: Huang Xiaolei , Zhang Cheng , Shang Xinci , Chen Yichang , Xiao Qin , Wei Zhengguo , Wang Guanghui , Zhen Xuechu , Xu Guoqiang , Min Jinrong , Shen Shaoming , Liu Yanli 
Published: December 2023

AbstractPTENα/β, two variants of PTEN, play a key role in promoting tumor growth by interacting with WDR5 through their N-terminal extensions (NTEs). This interaction facilitates the recruitment of the SET1/MLL methyltransferase complex, resulting in histone H3K4 trimethylation and upregulation of oncogenes such asNOTCH3, which in turn promotes tumor growth. However, the molecular mechanism underlying this interaction has remained elusive. In this study, we determined the crystal structure of PTENα-NTE in complex with WDR5, which reveal that PTENα specifically binds to the WIN site of WDR5 through a novel binding motif specifically found in the NTE domain of PTENα/β. Disruption of this interaction significantly impedes cell proliferation and tumor growth, highlighting the potential of the WIN site inhibitors of WDR5 as therapeutic agents for PTENα/β associated cancers. These findings not only shed light on the important role of the PTENα/β-WDR5 interaction in carcinogenesis, but also present a promising avenue for developing cancer treatments that target this pathway.
Oligonucleotide-based CRISPR-Cas9 toolbox for efficient engineering ofKomagataella phaffii
Authors: Strucko Tomas , Gadar-Lopez Adrian-E , Frøhling Frederik B , Frost Emma T , Olsson Helen , Jarczynska Zofia D , Mortensen Uffe H 
Published: December 2023

AbstractKomagataella phaffii(Pichia pastoris) is a methylotrophic yeast that is favored by industry and academia mainly for expression of heterologous proteins. However, its full potential as a host for bio-production of valuable compounds is not yet fully exploited. The emergence of CRISPR-Cas9 technology has significantly improved the efficiency of gene manipulations of non-conventional species includingK. phaffii. Yet, improvements in gene-editing methods are desirable to further accelerate engineering of industrially and scientifically relevantK. phaffiistrains. In this study, we have developed a versatile one vector-based CRISPR-Cas9 method and showed that it works efficiently at different genetic loci using linear DNA fragments with very short targeting sequences. Importantly, we show that by using our setup it is possible to catalyze single-stranded oligonucleotide-mediated mutagenesis and marker-free gene integrations. Notably, we performed site-specific point mutations and full gene deletions using single stranded 90-mers at very high efficiencies. Lastly, we present a strategy for transient inactivation of non-homologous end-joining (NHEJ) pathway, whereKU70gene is disrupted by a visual marker (uidAgene). The latter system enables precise CRISPR-Cas9 based editing (including multiplexing) and accelerates selection of the mutants that have simultaneously undergone a desired genetic modification(s) and restored NHEJ-proficient genotype. In conclusion, the tools presented in this study can be applied for easy and efficient engineering ofK. phaffiistrains and could potentially be coupled with high-throughput automated workflows.
EnsembleSeq: A workflow towards real-time, rapid and simultaneous multi-kingdom amplicon sequencing for holistic and cost-effective microbiome research at scale
Authors: Nagpal Sunil , Mande Sharmila S. , Hooda Harish , Dutta Usha , Taneja Bhupesh 
Published: December 2023

AbstractBackgroundBacterial communities are often concomitantly present with numerous microorganisms in the human body and other natural environments. Amplicon based microbiome studies have generally paid a skewed attention, that too at a rather shallow genus level resolution, to the highly abundant bacteriome, with interest now forking towards the other microorganisms, particularly fungi. Given the generally sparse abundance of other microbes in the total microbiome, simultaneous sequencing of amplicons targeting multiple microbial kingdoms could be possible even with full multiplexing. Guiding studies are currently needed for performing and monitoring multi-kingdom-amplicon sequencing and data capture at scale.MethodFull length bacterial 16S rRNA gene and entire fungal ITS region amplification was performed for human saliva samples (n=96, including negative and positive controls). Combined amplicon DNA libraries were prepared for nanopore sequencing using a major fraction of 16S molecules and a minor fraction of ITS amplicons. Sequencing was performed in a single run of an R10.4.1 flowcell employing the latest V14 chemistry. An approach for real time monitoring of the species saturation using dynamic rarefaction was designed as a guiding determinant of optimal run time.ResultsReal-time saturation monitoring for both bacterial and fungal species enabled the completion of sequencing within 30 hours, utilizing less than 60% of the total nanopores. ∼5 million HQ taxonomically assigned reads were generated (∼4.2 million bacterial and 0.7 million fungal), providing a wider (beyond bacteriome) snapshot of human oral microbiota at species level resolution. Among the more than 400 bacterial and 240 fungal species identified in the studied samples, the species of Streptococcus (e.g.S. mitis, S. oralis) and Candida (e.g.C. albicans, C. tropicalis) were observed to be the dominating microbes in the oral cavity, respectively. This conformed well with the previous reports of the human oral microbiota.ConclusionEnsembleseq provides a proof-of-concept towards identification of both fungal and bacterial species simultaneously in a single fully multiplexed nanopore sequencing run in a time and resource effective manner. Details of this workflow are provided to enable large scale application for a holistic species level microbiome study.
Structural basis of connexin-36 gap junction channel inhibition
Authors: Ding Xinyue , Aureli Simone , Vaithia Anand , Lavriha Pia , Schuster Dina , Khanppnavar Basavraj , Li Xiaodan , Blum Thorsten B. , Picotti Paola , Gervasio Francesco L. , Korkhov Volodymyr M. 
Published: December 2023

AbstractConnexin gap junction channels and hemichannels play important roles in intercellular communication and signaling. Some of connexin isoforms are associated with diseases, including hereditary neuropathies, heart disease and cancer. Although small molecule inhibitors of connexins show promise as therapeutic agents, the molecular mechanisms of connexin channel inhibition are unknown. Here, we report the cryo-EM structure of connexin-36 (Cx36) bound to an anti-malarial drug mefloquine at 2.1 Å resolution. Six drug binding sites partially occlude the pore of each connexon forming the channel. Each drug molecule in the ring makes contacts with residues in the pore-lining pocket and with the neighbouring mefloquine molecules, partially occluding the pore and modifying the pore electrostatics, ultimately reducing solute translocation through the channel. Structures of Cx36 in the presence of quinine and quinidine show a similar mode of drug binding. Molecular dynamics simulations of Cx36 bound to mefloquine show that drug binding affects the kinetics of ion passage through the pore. This previously undescribed mode of connexin channel inhibition presents an opportunity for designing subtype-specific connexin inhibitors.One-sentence summaryMechanism of connexin channel inhibition by small molecules