bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lanthanide-dependent isolation of phyllosphere methylotrophs selects for a phylogenetically conserved but metabolically diverse community
Authors: Govindaraju Alekhya M. , Friel Colleen A. , Good Nathan M. , Banks Sidney L. , Wayne Kenan S. , Martinez-Gomez N. Cecilia 
Published: June 2023

AbstractThe influence of lanthanide biochemistry during methylotrophy demands a reassessment of how the composition and metabolic potential of methylotrophic phyllosphere communities are affected by the presence of these metals. To investigate this, methylotrophs were isolated from soybean leaves by selecting for bacteria capable of methanol oxidation with lanthanide cofactors. Of the 344 pink-pigmented facultative methylotroph isolates, none were obligately lanthanide-dependent. Phylogenetic analyses revealed that all strains were nearly identical to each other and to model strains from theextorquensclade ofMethylobacterium, withrpoBproviding higher resolution than 16srRNA for strain-specific identification. Despite the low species diversity, the metabolic capabilities of the community diverged greatly. Strains encoding identical PQQ-dependent alcohol dehydrogenases displayed significantly different growth from each other on alcohols in the presence and absence of lanthanides. Several strains also lacked well-characterized lanthanide-associated genes thought to be important for phyllosphere colonization. Additionally, 3% of our isolates were capable of growth on sugars and 23% were capable of growth on aromatic acids, substantially expanding the range of multicarbon substrates utilized by members of theextorquensclade in the phyllosphere. Whole genome sequences of eleven novel strains are reported. Our findings suggest that the expansion of metabolic capabilities, as well as differential usage of lanthanides and their influence on metabolism among closely related strains, point to evolution of niche partitioning strategies to promote colonization of the phyllosphere.ImportanceLanthanides are essential metals for life. The identification of lanthanide-associated processes has been well-studied in methylotrophic bacteria, which are plant symbionts that utilize reduced one-carbon compounds for growth. Yet, the importance of lanthanides in plant-microbe interactions and the effects of lanthanides on microbial physiology and colonization in plants remains poorly understood. Here, we characterize the first methylotrophic bacterial community isolated from the phyllosphere in a lanthanide-dependent manner. We have identified strains encoding identical lanthanide-dependent enzymes yet exhibiting differences in lanthanide-associated growth, and have identified strains lacking lanthanide-associated genes thought to be important for phyllosphere colonization. In addition, we have identified many strains capable of metabolisms that were thought to be rare within this clade. Overall, our isolates serve as a microcosm by which to interrogate how lanthanides influence methylotrophic physiology in plant environments and highlights how phylogenetically similar strains can diverge greatly in metabolic potential.
Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM
Authors: Wankowicz Stephanie A. , Ravikumar Ashraya , Sharma Shivani , Riley Blake T. , Raju Akshay , Flowers Jessica , Hogan Daniel , van den Bedem Henry , Keedy Daniel A. , Fraser James S. 
Published: June 2023

AbstractIn their folded state, biomolecules exchange between multiple conformational states that are crucial for their function. Traditional structural biology methods, such as X-ray crystallography and cryogenic electron microscopy (cryo-EM), produce density maps that are ensemble averages, reflecting molecules in various conformations. Yet, most models derived from these maps explicitly represent only a single conformation, overlooking the complexity of biomolecular structures. To accurately reflect the diversity of biomolecular forms, there is a pressing need to shift towards modeling structural ensembles that mirror the experimental data. However, the challenge of distinguishing signal from noise complicates manual efforts to create these models. In response, we introduce the latest enhancements to qFit, an automated computational strategy designed to incorporate protein conformational heterogeneity into models built into density maps. These algorithmic improvements in qFit are substantiated by superior Rfreeand geometry metrics across a wide range of proteins. Importantly, unlike more complex multicopy ensemble models, the multiconformer models produced by qFit can be manually modified in most major model building software (e.g. Coot) and fit can be further improved by refinement using standard pipelines (e.g. Phenix, Refmac, Buster). By reducing the barrier of creating multiconformer models, qFit can foster the development of new hypotheses about the relationship between macromolecular conformational dynamics and function.
A cellular and spatial atlas ofTP53-associated tissue remodeling in lung adenocarcinoma
Authors: Zhao William , Kepecs Benjamin , Mahadevan Navin R. , Segerstolpe Asa , Weirather Jason L. , Besson Naomi R. , Giotti Bruno , Soong Brian Y. , Li Chendi , Vigneau Sebastien , Slyper Michal , Wakiro Isaac , Jane-Valbuena Judit , Ashenberg Orr , Rotem Asaf , Bueno Raphael , Rozenblatt-Rosen Orit , Pfaff Kathleen , Rodig Scott , Hata Aaron N. , Regev Aviv , Johnson Bruce E. , Tsankov Alexander M. 
Published: June 2023

ABSTRACTTP53is the most frequently mutated gene across many cancers and is associated with shorter survival in lung adenocarcinoma (LUAD). To define howTP53mutations affect the LUAD tumor microenvironment (TME), we constructed a multi-omic cellular and spatial tumor atlas of 23 treatment-naïve human lung tumors. We found thatTP53-mutant (TP53mut) malignant cells lose alveolar identity and upregulate highly proliferative and entropic gene expression programs consistently across resectable LUAD patient tumors, genetically engineered mouse models, and cell lines harboring a wide spectrum ofTP53mutations. We further identified a multicellular tumor niche composed ofSPP1+macrophages and collagen-expressing fibroblasts that coincides with hypoxic, pro-metastatic expression programs inTP53muttumors. Spatially correlated angiostatic and immune checkpoint interactions, includingCD274-PDCD1andPVR-TIGIT, are also enriched inTP53mutLUAD tumors, which may influence response to checkpoint blockade therapy. Our methodology can be further applied to investigate mutation-specific TME changes in other cancers.
CoPheScan: phenome-wide association studies accounting for linkage disequilibrium
Authors: Manipur Ichcha , Reales Guillermo , Sul Jae Hoon , Shin Myung Kyun , Longerich Simonne , Cortes Adrian , Wallace Chris 
Published: June 2023

AbstractPhenome-wide association studies (PheWAS) facilitate the discovery of associations between a single genetic variant with multiple phenotypes. For variants which impact a specific protein, this can help identify additional therapeutic indications or on-target side effects of intervening on that protein. However, PheWAS is restricted by an inability to distinguish confounding due to linkage disequilibrium (LD) from true pleiotropy. Here we describe CoPheScan (Coloc adapted Phenome-wide Scan), a Bayesian approach that enables an intuitive and systematic exploration of causal associations while simultaneously addressing LD confounding. We demonstrate its performance through simulation, showing considerably better control of false positive rates than a conventional approach not accounting for LD. We used CoPheScan to perform PheWAS of protein-truncating variants and fine-mapped variants from disease and pQTL studies, in 2275 disease phenotypes from the UK Biobank. Our results identify the complexity of known pleiotropic genes such asAPOE, and suggest a new causal role forTGM3in skin cancer.
Sse1, Hsp110 chaperone of yeast, controls the cellular fate during Endoplasmic Reticulum-stress
Authors: Jha Mainak Pratim , Kumar Vignesh , Sharma Lakshita , Ghosh Asmita , Mapa Koyeli 
Published: June 2023

AbstractSse1 is a cytosolic Hsp110 molecular chaperone of yeast,Saccharomyces cerevisiae. Its multifaceted roles in cellular protein homeostasis as Nucleotide Exchange Factor (NEF), as protein-disaggregase and as a Chaperone linked to Protein Synthesis (CLIPS), are well documented. In the currently study, we show thatSSE1genetically interacts withIRE1andHAC1, the Endoplasmic Reticulum-Unfolded Protein Response (ER-UPR) sensors implicating its role in ER protein homeostasis. Interestingly, absence of this chaperone imparts unusual resistance to tunicamycin-induced ER stress which depends on the intact Ire1-Hac1 mediated ER-UPR signalling. Furthermore, cells lackingSSE1show ER-stress-responsive inefficient reorganization of translating ribosomes from polysomes to monosomes and increased monosome content that drive uninterrupted protein translation. In consequence, the kinetics of ER-UPR is starkly different insse1Δ strain where we show that stress response induction and restoration of homeostasis is prominently faster in contrast to the wildtype (WT) cells. Importantly, Sse1 plays a critical role in controlling the ER-stress mediated cell division arrest which is escaped insse1Δ strain during chronic tunicamycin stress. Consequently,sse1Δ strain shows significantly higher cell viability in comparison to WT yeast, following short-term as well as long-term tunicamycin stress. In summary, we demonstrate a new role of Sse1 in ER protein homeostasis where the chaperone genetically interacts with ER-UPR pathway, controls the protein translation during ER stress and the kinetics of ER-UPR. More importantly, we show the crtical role of Sse1 in regulating the ER-stress-induced cell division arrest and cell death during global ER stress by tunicamycin.Author SummarySse1 is a cytosolic Hsp110 molecular chaperone of yeast,Saccharomyces cerevisiae. It performs various functions as Nucleotide Exchange Factor (NEF), as a protein-disaggregase and as a Chaperone linked to Protein Synthesis (CLIPS) to maintain a healthy proteome in the cytosol. In the present study, we show thatSSE1is a critical player to maintain Endoplasmic Reticulum (ER) protein homeostasis. We report thatSSE1genetically interacts with the ER-Unfolded Protein Response (ER-UPR) sensors,IRE1andHAC1. In absence ofSSE1,yeast cells gain unusual fitness to tunicamycin (Tm)-induced ER stress which depends on the functional Ire1-Hac1 mediated ER-UPR signalling. Furthermore, Sse1 controls the ribosomal organization during tunicamycin-induced ER-stress and in absence of the chaperone the amount of polysomes and monosmes are high leading to uninterrupted protein translation during ER stress. Consequently,sse1Δ strain exhibits starkly different ER-UPR kinetics compared to wildtype (WT) cells. Importantly, our data reveal that cell division arrest and cell death due to Tm-induced ER-stress is critically controlled by Sse1.
Repurposing the dark genome. IV – noncoding proteins
Authors: Nayak Sarangdhar , Dhar Pawan K. 
Published: June 2023

AbstractThe dark genome comprising of non-expressing, non-translating, and extinct DNA sequences has remained a largely unexplored genomic space. Using computational and experimental approaches, novel insights into the dark matter genome have recently been gained, revealing the presence of a vast and unexplored resource. Non-coding RNA (ncRNA) refers to a class of RNA molecules that do not encode proteins but play important regulatory roles in the cell. We asked if it was possible to make functional peptides and proteins from ncRNA leading to a new biological insight and applications? Here we present initial computational data in support of making functional noncoding proteins (NCP) from ncRNA sequences. Different types of non-coding genomic sequences originating fromCaenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, andHomo sapienswere studied to understand sequence composition, secondary structure, and physiochemical properties of NCPs. This work builds the foundation for experimentally characterizing the first-in-the-class non-coding proteins leading to a novel insights and applications.
A SEVA-based, CRISPR-Cas3-assisted genome engineering approach forPseudomonaswith efficient vector curing
Authors: Lammens Eveline-Marie , Volke Daniel Christophe , Schroven Kaat , Voet Marleen , Kerremans Alison , Lavigne Rob , Hendrix Hanne 
Published: June 2023

AbstractThe development of CRISPR-Cas-based engineering technologies has revolutionized the microbial biotechnology field. Over the years, the Class II Type II CRISPR-Cas9 system has become the gold standard for genome editing in many bacterial hosts. However, the Cas9 system does not allow efficient genomic integration inPseudomonas putida, an emerging Synthetic Biology host, without the assistance of lambda-Red recombineering. In this work, we utilize the alternative Class I Type I-C CRISPR-Cas3 system fromPseudomonas aeruginosaas a highly-efficient genome editing tool forP. putidaandP. aeruginosa. This system consists of two vectors, one encoding the Cas genes, CRISPR array and targeting spacer, and a second SEVA-vector, containing the homologous repair template. Both vectors are Golden Gate compatible for rapid cloning and are available with multiple antibiotic markers, for application in various Gram-negative hosts and different designs. By employing this Cas3 system, we successfully integrated an 820-bp cassette in the genome ofP. putidaand performed several genomic deletions inP. aeruginosawithin four days, with an efficiency of >83% for both hosts. Moreover, by introducing a universal self-targeting spacer, the Cas3 system rapidly cures all helper vectors, including itself, from the host strain in a matter of days. As such, this system constitutes a valuable engineering tool forPseudomonas, to complement the existing range of Cas9-based editing methods and facilitates genomic engineering efforts of this important genus.ImportanceThe CRISPR-Cas3 editing system as presented here facilitates the creation of genomic alterations inP. putidaandP. aeruginosain a straightforward manner. By providing the Cas3 system as a vector set with Golden Gate compatibility and different antibiotic markers, as well as by employing the established SEVA vector set to provide the homology repair template, this system is flexible and can readily be ported to a multitude of Gram-negative hosts. Besides genome editing, the Cas3 system can also be used as an effective and universal tool for vector curing. This is achieved by introducing a spacer that targets theoriT, present on the majority of established (SEVA) vectors. Based on this, the Cas3 system efficiently removes up to three vectors in only a few days. As such, this curing approach may also benefit other genomic engineering methods or remove naturally-occurring plasmids from bacteria.
PAS domain of flagellar histidine kinase FlrB exhibits novel architecture, and binds Heme as sensory signal in unconventional fashion
Authors: Mukherjee Peeali , Agarwal Shubhangi , Basu Mallick Sritapa , Dasgupta Jhimli 
Published: June 2023

SUMMARYPhosphorylation of the σ54-dependent transcription activator FlrC by the sensor histidine kinase FlrB is essential in flagellar synthesis ofVibrio cholerae. Despite that, the structure, sensory signal, and mechanistic basis of function of FlrB were elusive. Here we report the crystal structure of the sensory PAS domain of FlrB in functional dimeric state that exhibits a novel architecture. Series of biochemical/biophysical experiments unequivocally established heme as sensory ligand that packs hydrophobically in the ligand binding cleft of FlrB-PAS. Intriguingly, ATP binding to the C-terminal ATP binding (CA) domain assists PAS domain to bind heme, vis-à-vis, heme binding to the PAS facilitates ATP binding to CA; suggesting a synergistic mode of heme and ATP binding to FlrB. We propose that such synergistic binding triggers conformational signaling in FlrB, leading to the downstream flagellar gene transcription. Enhanced swimming motility ofV. choleraewith increased heme uptake further supports this proposition.
The Cognitive Critical Brain: Modulation of Criticality in Task-Engaged Regions
Authors: Liu Xingyu , Fei Xiaotian , Liu Jia 
Published: June 2023

ABSTRACTThe constantly evolving world necessitates a brain that can adapt and respond to rapid changes. The brain, conceptualized as a system performing cognitive functions through collective neural activity, has been shown to maintain a resting state characterized by near-critical neural activity, poised to respond to external stimuli. The dynamic adaptation of nearcriticality during various tasks, however, remains poorly understood. In this study, we utilized the prototypical Hamiltonian Ising model to investigate the modulation of near-criticality in neural activity at the cortical subsystem level during cognitive tasks. Specifically, we theoretically simulated cortical 2D-Ising modelsin silicousing structural MRI data and empirically estimated the system statein vivousing functional MRI data. First, our findings corroborated previous studies that the resting state is typically near-critical as captured by the Ising model. Notably, we found that cortical subsystems changed their criticality levels heterogeneously during a naturalistic movie-watching task, where visual and auditory cortical regions were fine-tuned closer to criticality. A more fine-grained analysis of the ventral temporal cortex during an object recognition task revealed that only regions selectively responsive to a specific object category were tuned closer to criticality when processing that object category. In conclusion, our study supports thecognitive critical brain hypothesisthat modulating the criticality of subsystems within the hierarchical modular brain may be a general mechanism for achieving diverse cognitive functions.
Five ways to waste food: food wasting behaviours questionnaire
Authors: Misiak Michal , Sobol Malgorzata , Sakowski Lukasz , Kowal Marta , Jurczyk Aleksandra , Wojtycka Lidia 
Published: June 2023

PurposeThe goal of the present research was to resolve two problems with contemporary methods used to assess consumer food waste: the lack of established categories of food wasting behaviours and difficulties in assessing food waste. In Studies 1 A and 1 B, a five-factor questionnaire for measuring food wasting behaviours was developed. Study 2 and Exploratory analyses verified whether the questionnaire allows for predicting the amount of wasted meat, dairy and bakery and a range of socioeconomic characteristics.Design/methodology/approachBased on pre-registered studies, a new questionnaire for measuring the frequency of food wasting behaviours, the Food Wasting Behaviours Questionnaire (FWBQ), was developed.FindingsThe results provided evidence that behaviours associated with food wasting could be narrowed down to five distinctive basic categories: (1) discarding food because of its' unpalatability; (2) preventing food waste through buying only the necessities; (3) preventing food waste through planning; (4) preventing food waste through sharing and (5) preventing food waste through feeding animals. The FWBQ allowed for investigating the socio-economic factors that influence food wasting behaviour. Finally, the FWBQ allowed for predicting the amount of wasted meat, dairy and bakery products. Also, particular factors were associated with a range of socioeconomic characteristics.Originality/valueThe FWBQ has been shown to be an inexpensive and easy-to-use method for systematising distinct categories of food wasting behaviours and demonstrating their determinants. The study takes an empirical approach (rather than intuitive) to distinguish separate categories of food wasting.
An overview of applications and trends in the use of extended reality for teaching effectiveness: an umbrella review based on 20 meta-analysis studies
Authors: Dong Wei , Zhou Meimei , Zhou Meiyan , Jiang Bihan , Lu Jijian 
Published: June 2023

Purpose
The purpose of this paper is to study the application ways of extended reality (XR) in teaching, the specific teaching effects and how to implement teaching integration.

Design/methodology/approach
The study adopts an umbrella review approach, locates and screens 20 pertinent meta-analysis studies published in international journals and conducts a systematic review of the effects of teaching applications of XR technologies in terms of subject categories, education levels and teaching cycles.

Findings
The study finds that the effects of virtual reality and augmented reality technologies on teaching effectiveness can reach up to 0.723 and 0.951, indicating that XR technologies can improve teaching.

Practical implications
Through the systematic analysis of 20 related element analysis studies published in international journals, the specific methods and effects of XR technology applied to teaching are finally obtained and put forward the new application trend of XR promoting teaching effect.

Originality/value
In the past decade, more and more research has also focused on the specific methods and effects of XR technology applied to teaching. However, there are still problems such as unclear technology application path and unclear effect. Based on this, it is necessary to further conduct an overall overview and analysis of the impact of XR technology on teaching effect when it is integrated into teaching, systematically study the teaching effect of XR technology in different education levels and subject types and provide a theoretical basis for more detailed research on XR technology integration into teaching.