bluuebunny/crossref_metadata_2025 huggingface dataset:
Antagonistic effects of arginine methylation of LSM4 on alternative splicing during plant stress responses
Authors: Agrofoglio Yamila Carla , Iglesias María José , Perez-Santángelo Soledad , José de Leone María , Koester Tino , Catalá Rafael , Salinas Julio , Yanovsky Marcelo J. , Staiger Dorothee , Mateos Julieta L.
Published: December 2023

Arabidopsis PROTEIN ARGININE METHYLTRANSFERASE 5 (PRMT5) post-translationally modifies RNA-binding proteins by arginine (R) methylation. The impact of this modification on the regulation of RNA processing is largely unknown. Here we use LSM4, a component of the spliceosome, as a paradigm to study the impact of R-methylation on its function in RNA processing. We identify in vivo targets of LSM4 and show that LSM4 regulates alternative splicing of a suite of them. Furthermore, LSM4 affects mRNA levels of some of the targets, showing for the first time its role in both AS and steady-state abundance. Thelsm4andprmt5mutants show a considerable overlap of genes with altered splicing patterns, suggesting that these might be regulated by PRMT5-dependent LSM4 methylation. Wild-type LSM4 and an unmethylable version complement thelsm4-1growth and circadian rhythms defects, suggesting that methylation is not critical for growth in normal environments. However, LSM4 methylation increases with ABA and is necessary for plants to respond properly to salt stress. In contrast, LSM4 methylation is reduced by bacterial infection, and plants expressing unmethylable LSM4 are more resistant than plants expressing wild-type LSM4. This tolerance correlates with decreased intron retention of immune-response genes upon infection, augmenting the functional isoform. Taken together, this provides the first direct evidence that R methylation adjusts LSM4 function on pre-mRNA splicing in an antagonistic manner in response to biotic and abiotic stress.

Highlight

Please provide a statement that, in fewer than 30 words, highlights the novelty of the paper for the non-expert.

Arginine methylation of the LSM4 spliceosome component by PROTEIN ARGININE METHYLTRANSFERASE 5 fine-tunes alternative splicing of a set of stress-related genes to antagonistically control biotic and abiotic responses in Arabidopsis.
Concurrent threats and extinction risk in a long-lived, highly fecund vertebrate with parental care
Authors: Brooks George C. , Hopkins William A. , Kindsvater Holly K.
Published: December 2023

Detecting declines and quantifying extinction risk of long-lived, highly fecund vertebrates including fishes, reptiles, and amphibians, can be challenging. In addition to the false notion that large clutches always buffer against population declines, the imperiled status of long-lived species can often be masked by extinction debt, wherein adults persist on the landscape for several years after populations cease to be viable. Here we develop a demographic model for the Eastern Hellbender (Cryptobranchus alleganiensis), an imperiled aquatic salamander with paternal care. We examined the individual and interactive effects of three of the leading threats hypothesized to contribute to the species’ demise: habitat loss due to siltation, high rates of nest failure, and excess adult mortality caused by fishing and harvest. We parameterized the model using data on their life history and reproductive ecology to model the fates of individual nests and address multiple sources of density-dependent mortality under both deterministic and stochastic environmental conditions. Our model suggests that high rates of nest failure observed in the field are sufficient to drive hellbender populations towards a geriatric age distribution and eventually to localized extinction, but that this process takes decades. Moreover, the combination of limited nest site availability due to siltation, nest failure, and stochastic adult mortality can interact to increase the likelihood and pace of extinction, which was particularly evident under stochastic scenarios. Density-dependence in larval survival and recruitment can severely hamper a population’s ability to recover from declines. Our model helps to identify tipping points beyond which extinction becomes certain and management interventions become necessary. Our approach can be generalized to understand the interactive effects of various threats to the extinction risk of other long-lived vertebrates. As we face unprecedented rates of environmental change, holistic approaches incorporating multiple concurrent threats and their impacts on different aspects of life history will be necessary to proactively conserve long-lived species.
High-resolution awake mouse fMRI at 14 Tesla
Authors: Hike David , Liu Xiaochen , Xie Zeping , Zhang Bei , Choi Sangcheon , Zhou Xiaoqing Alice , Liu Andy , Murstein Alyssa , Jiang Yuanyuan , Devor Anna , Yu Xin
Published: December 2023

High-resolution awake mouse fMRI remains challenging despite extensive efforts to address motion-induced artifacts and stress. This study introduces an implantable radiofrequency (RF) surface coil design that minimizes image distortion caused by the air/tissue interface of mouse brains while simultaneously serving as a headpost for fixation during scanning. Furthermore, this study provides a thorough acclimation method used to accustom animals to the MRI environment minimizing motion induced artifacts. Using a 14T scanner, high-resolution fMRI enabled brain- wide functional mapping of visual and vibrissa stimulation at 100x100x200µm resolution with a 2s per frame sampling rate. Besides activated ascending visual and vibrissa pathways, robust BOLD responses were detected in the anterior cingulate cortex upon visual stimulation and spread through the ventral retrosplenial area (VRA) with vibrissa air-puff stimulation, demonstrating higher-order sensory processing in association cortices of awake mice. In particular, the rapid hemodynamic responses in VRA upon vibrissa stimulation showed a strong correlation with the hippocampus, thalamus, and prefrontal cortical areas. Cross-correlation analysis with designated VRA responses revealed early positive BOLD signals at the contralateral barrel cortex (BC) occurring 2 seconds prior to the air-puff in awake mice with repetitive stimulation, which was not detected using a randomized stimulation paradigm. This early BC activation indicated a learned anticipation through the vibrissa system and association cortices in awake mice under continuous training of repetitive air-puff stimulation. This work establishes a high-resolution awake mouse fMRI platform, enabling brain-wide functional mapping of sensory signal processing in higher association cortical areas.

Significance Statement

This awake mouse fMRI platform was developed by implementing an advanced implantable radiofrequency (RF) coil scheme, which simultaneously served as a headpost to secure the mouse head during scanning. A thorough acclimation method was used to accustom animals to the MRI environment minimizing motion induced artifacts. The ultra-high spatial resolution (100x100x200µm) BOLD fMRI enabled the brain-wide mapping of activated visual and vibrissa systems during sensory stimulation in awake mice, including association cortices, e.g. anterior cingulate cortex and retrosplenial cortex, for high order sensory processing. Also, the activation of barrel cortex at 2 s prior to the air-puff indicated a learned anticipation of awake mice under continuous training of the repetitive vibrissa stimulation.
Collective directional memory controls the range of epithelial cell migration
Authors: Canever Helena , Lachuer Hugo , Delaunay Quentin , Sipieter François , Audugé Nicolas , Girard Philippe P. , Borghi Nicolas
Published: December 2023

Cell migration is a fundamental behavior involved in multicellular development, regeneration, and homeostasis, which is deregulated in cancer. Epithelial cells migrate individually when isolated and collectively within a tissue. However, how interactions between cells affect their ability to explore space and their sensitivity to guidance signals is poorly understood. Here, we show that isolated cells that are persistent random walkers adopt a superdiffusive behavior in an epithelium. The effect is stronger than external guidance cues and enables cells to reach greater distances than when isolated. This directional memory emerges from fractional Brownian motion that relies on velocity coordination between neighboring cells with intact cytoskeletal connections to intercellular adhesion complexes. Furthermore, we show how the stability and mechanosensitivity of adhesion complexes ultimately regulate the speed of collective migration and the sensitivity to guidance signals via dimerization of the adhesion protein vinculin. Together, our results show how cell speed, persistence, and directionality define the efficiency of spatial cell exploration on short, intermediate, and long time scales, respectively.
VviWRKY10andVviWRKY30co-regulate powdery mildew resistance through modulating SA and ET-based defenses in grapevine
Authors: Zhou Min , Wang Hongyan , Yu Xuena , Cui Kaicheng , Hu Yang , Xiao Shunyuan , Wen Ying-Qiang
Published: December 2023

ABSRACT

Grapevine is one of the most important economic fruit crops in the world. The widely cultivated grapevine (Vitis vinifera,Vvi) is susceptible to powdery mildew caused byErysiphe necator. In this study, CRISPR-Cas9 was used to simultaneously knock outVviWRKY10andVviWRKY30encoding two transcription factors reported to be implicated in defense regulation. Fifty-threewrky10(Vviwrky10single mutant) transgenic plants and fifteenwrky10wrky30(Vviwrky10Vviwrky30double mutant) transgenic plants were generated. In a 2-year field evaluation of resistance to powdery mildew, thewrky10showed strong resistance, while thewrky10wrky30showed moderate resistance. Further analyses revealed that salicylic acid (SA) and reactive oxygen species (ROS) contents in the leaves ofwrky10andwrky10wrky30were significantly increased, so did the ethylene (ET) content in the leaves ofwrky10. The results from dual luciferase (DLUC) reporter assays, electrophoretic mobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP)-qPCR assays demonstrated that VviWRKY10 could directly bind to the W-boxes in the promoter ofVviEDS5-2,VviPR1,VviPR5andVviRBOHD2and inhibit their transcription, supporting its role as a negative regulator of SA-dependent defense. By contrast, VviWRKY30 could directly bind to the W-boxes in the promoter ofVviACS3andVviACS3Land promote their transcription, playing a positive role in ET production and ET-dependent defense. Moreover, VviWRKY10 and VviWRKY30 can bind to each other’s promoters and mutually inhibit each other’s transcription. Taken together, our results have revealed a complex mechanism of regulation by VviWRKY10 and VviWRKY30 for activation of measured and balanced defense responses against powdery mildew in grapevine.

One-sentence summary

VviWRKY10andVviWRKY30play different roles in powdery mildew resistance through the salicylic acid and ethylene, respectively, and there is mutual inhibition betweenVviWRKY10andVviWRKY30.
StrengtheningBordetella pertussisgenomic surveillance by direct sequencing of residual positive specimens
Authors: Peng Yanhui , Williams Margaret M. , Xiaoli Lingzi , Simon Ashley , Fueston Heather , Tondella M. Lucia , Weigand Michael R.
Published: December 2023

Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here we report a novel culture-independent approach to genome characterization ofBordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA “baits” targetingB. pertussisfragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery ofB. pertussisgenome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased yield ofB. pertussissequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms (wgSNP) and whole-genome multilocus sequencing typing (wgMLST). Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with IS481Ct < 35 and > 10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.
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

The 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.

Importance

This 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

The 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

Efficient 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

Rapid 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

GPR68 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

Deep 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

Background

Artificial 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 Findings

This 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.

Conclusions

This 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

Background

In 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.

Methods

The 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.

Results

The 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.

Conclusion

This 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

PTENα/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

Komagataella 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

Background

Bacterial 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.

Method

Full 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.

Results

Real-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.

Conclusion

Ensembleseq 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

Connexin 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 summary

Mechanism of connexin channel inhibition by small molecules
AI without networks
Authors: Mitra Partha P. , Sire Clément
Published: December 2023

Contemporary Artificial Intelligence (AI) stands on two legs: large training data corpora and many-parameter artificial neural networks (ANNs). The data corpora are needed to represent the complexity and heterogeneity of the world. The role of the networks is less transparent due to the obscure dependence of the network parameters and outputs on the training data and inputs. This raises problems, ranging from technical-scientific to legal-ethical. We hypothesize that a transparent approach to machine learning is possible without using networks at all. By generalizing a parameter-free, statistically consistent data interpolation method, which we analyze theoretically in detail, we develop a network-free framework for AI incorporating generative modeling. We demonstrate this framework with examples from three different disciplines - ethology, control theory, and mathematics. Our generative Hilbert framework applied to the trajectories of small groups of swimming fish outperformed state-of-the-art traditional mathematical behavioral models and current ANN-based models. We demonstrate pure data interpolation based control by stabilizing an inverted pendulum and a driven logistic map around unstable fixed points. Finally, we present a mathematical application by predicting zeros of the Riemann Zeta function, achieving comparable performance as a transformer network. We do not suggest that the proposed framework will always outperform networks as over-parameterized networks can interpolate. However, our framework is theoretically sound, transparent, deterministic, and parameter free: remarkably, it does not require any compute-expensive training, does not involve optimization, has no model selection, and is easily reproduced and ported. We also propose an easily computed method of credit assignment based on this framework, to help address ethical-legal challenges raised by generative AI.
Building information modeling (BIM) in green buildings: a state-of-the-art bibliometric review
Authors: Fauzi Muhammad Ashraf , Anuar Khairul Firdaus , Mohd Zainudin Nurhaizan , Ahmad Mohd Hanafiah , Wider Walton
Published: December 2023

Purpose

This study evaluates the knowledge structure of building information modeling (BIM) in green buildings. Buildings are one of the main contributors to carbon emissions, and implementing BIM in green buildings is seen as an indispensable approach to mitigate environmental and climate change issues.

Design/methodology/approach

Through a bibliometric analysis, 297 publications retrieved from the Web of Science (WoS) were analyzed to explore their intellectual structure.

Findings

Bibliographic coupling analysis produced four clusters on current and emerging trends, while co-word analysis produced four clusters on future BIM and green building trends. Current and emerging trends revolve around BIM adoption in green and existing buildings, life cycle analysis (LCA) and sustainable rating tools. Future trends related to BIM and performance analysis and optimization, the BIM framework for green building design and construction, overcoming barriers and maximizing benefits in BIM adoption.

Research limitations/implications

The implications of this study are relevant to all BIM and green building stakeholders, including developers, engineers, architects, occupants, tenants and the whole community.

Originality/value

This study examines the crucial integration of BIM and green building within the more extensive construction and building field scope.
Does the pandemic disrupt the livelihoods of marine fishermen? Evidence from Kerala during the pre- and post-lockdown periods of Covid-19
Authors: Suresh P.R.
Published: December 2023

Purpose

This paper aims to determine the implications of Covid-19 on the livelihood of marine fishermen. It gives a concrete picture of how vulnerable communities like marine fishermen are affected due to the lockdown policies. The paper examines these communities' present status and the extent of vulnerability during the post-Covid period.

Design/methodology/approach

The study uses an exploratory research design to find the solution to the research problem. 298 samples were collected and analysed within a sustainable livelihood theoretical framework. The scope of the study is limited to marine fishermen in Kerala, residing in six districts out of the nine coastal districts. The impact of the lockdown on income was analysed using paired t-test and results linked with the theory.

Findings

The study has done an empirical analysis for three periods: before lockdown, lockdown and after lockdown, to identify the impact of lockdown on marine fishermen. The study's significant findings are that these fishermen's livelihood is at risk during the post-lockdown period, and many families are moving into a “debt-trap”.

Research limitations/implications

Policymakers can develop appropriate policy strategies to enhance the livelihood assets of vulnerable communities to include them in a sustainable framework.

Originality/value

Only a few studies are highlighting the impact of Covid-19 on vulnerable communities in India. The effects of climate change on the marine ecosystem are already endangering marine fisher folks' livelihoods. In this light, it is vital to study the extent of the impact of income shock on the livelihood assets of marine fishermen due to the lockdown policy implemented in the State to prevent the spread of Covid-19.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-03-2023-0192
Economic policy uncertainty and cost rigidity: the moderating effects of government contracts and political connections
Authors: Kim Hoyoung , Harjoto Maretno Agus
Published: December 2023

Purpose

This study examines the relationship between economic policy uncertainty (EPU) and managers' ex ante strategic choice on firms’ fixed and variable costs structure, i.e. cost rigidity and the moderating effect of government contracts and political connections.

Design/methodology/approach

Using a sample of 4,162 US firms during 2003–2019 and EPU measure from Baker et al. (2016), the authors examine the association between EPU and cost rigidity using multivariate regression analysis. The authors also examine the moderating effects of government customers and political connections using the subsampling method.

Findings

This study finds that increases in EPU leads to higher cost rigidity, suggesting that managers tend to look ahead and make an ex ante commitment to invest more in fixed costs to avoid congestion costs in anticipation of future product demand during EPU. The study also finds that the presence of government customers and political connections moderates the need for adopting greater cost rigidity.

Research limitations/implications

This study measures firms' cost rigidity based on archival data. Future studies could utilize managers' cost structure choices using firms' internal management cost structure forecasts data to measure cost rigidity to examine the relationship between cost rigidity and EPU.

Practical implications

This study demonstrates that managers tend to make a proactive commitment to invest in fixed inputs when facing demand uncertainty from EPU to avoid congestion costs. This study also highlights the value of having government contracts and political connections by demonstrating that managers are less concerned about the congestion costs, hence weakening the impact of EPU on cost rigidity when they have government as major customers and/or political connections.

Originality/value

This study extends the management accounting literature by documenting that cost rigidity is related to EPU and that the relationship between cost rigidity and EPU also depends on whether the firm has government as major customers and/or political connections or not.
Collaborative government-public efforts in driving green technology innovation for environmental governance in PPP projects: a study based on prospect theory
Authors: Bu Zehui , Liu Jicai , Zhang Xiaoxue
Published: December 2023

Purpose

The paper aims to elucidate effective strategies for promoting the adoption of green technology innovation within the private sector, thereby enhancing the value of public–private partnership (PPP) projects during the operational phase.

Design/methodology/approach

Utilizing prospect theory, the paper considers the government and the public as external driving forces. It establishes a tripartite evolutionary game model composed of government regulators, the private sector and the public. The paper uses numerical simulations to explore the evolutionary stable equilibrium strategies and the determinants influencing each stakeholder.

Findings

The paper demonstrates that government intervention and public participation substantially promote green technology innovation within the private sector. Major influencing factors encompass the intensity of pollution taxation, governmental information disclosure and public attention. However, an optimal threshold exists for environmental publicity and innovation subsidies, as excessive levels might inhibit technological innovation. Furthermore, within government intervention strategies, compensating the public for their participation costs is essential to circumvent the public's “free-rider” tendencies and encourage active public collaboration in PPP project innovation.

Originality/value

By constructing a tripartite evolutionary game model, the paper comprehensively examines the roles of government intervention and public participation in promoting green technology innovation within the private sector, offering fresh perspectives and strategies for the operational phase of PPP projects.