bluuebunny/crossref_metadata_2025 huggingface dataset:
Propionyl-CoA carboxylase subunit B regulates anti-tumor T cells in a pancreatic cancer mouse model
Authors: Han Han V. , Efem Richard , Rosati Barbara , Lu Kevin , Maimouni Sara , Jiang Ya-Ping , Montoya Valeria , Van Der Velden Adrianus W. M. , Zong Wei-Xing , Lin Richard Z.
Published: July 2023

Most human pancreatic ductal adenocarcinoma (PDAC) are not infiltrated with cytotoxic T cells and are highly resistant to immunotherapy. Over 90% of PDAC have oncogenic KRAS mutations, and phosphoinositide 3-kinases (PI3Ks) are direct effectors of KRAS. Our previous study demonstrated that ablation ofPik3cain KPC (KrasG12D;Trp53R172H;Pdx1-Cre) pancreatic cancer cells induced host T cells to infiltrate and completely eliminate the tumors in a syngeneic orthotopic implantation mouse model. Now, we show that implantation ofPik3ca-/-KPC (named αKO) cancer cells induces clonal expansion of cytotoxic T cells infiltrating the pancreatic tumors. To identify potential molecules that can regulate the activity of these anti-tumor T cells, we conducted anin vivogenome-wide gene-deletion screen using αKO cells implanted in the mouse pancreas. The result shows that deletion of propionyl-CoA carboxylase subunit B gene (Pccb) in αKO cells (named p-αKO) leads to immune evasion, tumor progression and death of host mice. Surprisingly, p-αKO tumors are still infiltrated with clonally expanded CD8+T cells but they are inactive against tumor cells. However, blockade of PD-L1/PD1 interaction reactivated these clonally expanded T cells infiltrating p-αKO tumors, leading to slower tumor progression and improve survival of host mice. These results indicate thatPccbcan modulate the activity of cytotoxic T cells infiltrating some pancreatic cancers and this understanding may lead to improvement in immunotherapy for this difficult-to-treat cancer.
Coding dynamics of the striatal networks during learning
Authors: Villet Maxime , Reynaud-Bouret Patricia , Poitreau Julien , Baldi Jacopo , Jaffard Sophie , James Ashwin , Muzy Alexandre , Sargolini Francesca , Bethus Ingrid
Published: July 2023

The rat dorsomedial (DMS) and dorsolateral striatum (DMS), equivalent to caudate nucleus and putamen in primates, are generally required for goal-directed and habit behaviour, respectively. However, it is still unclear whether and how this functional dychotomy emerges in the course of learning. In this study we investigated this issue by recording DMS and DLS single neuron activity in rats performing a continuous spatial alternation task, from the acquisition to optimized performance. We first applied a classical analytical approach to identify task-related activity based on the modifications of single neuron firing rate in relation to specific task events or maze trajectories. We then used an innovative approach based on Hawkes process to reconstruct a directed connectivity graph of simultaneously recorded neurons, that was used to decode animal behavior. This approach enabled us to better unravel the role of DMS and DLS neural networks across learning stages. We showed that DMS and DLS display different task-related activity throughout learning stages, and the proportion of coding neurons over time decreases in the DMS and increases in the DLS. Despite theses major differences, the decoding power of both networks increases during learning. These results suggest that DMS and DLS neural networks gradually reorganize in different ways in order to progressively increase their control over the behavioral performance.
The influence of carbon dioxide on cerebral metabolism and oxygen consumption: combining multimodal monitoring with dynamic systems modelling
Authors: Highton David , Caldwell Matthew , Tachtsidis Ilias , Elwell Clare E , Smith Martin , Cooper Chris E
Published: July 2023

Hypercapnia increases cerebral blood flow, but the effect on cerebral metabolism in humans remains incompletely understood. Either increased or reduced oxygen consumption has been predicted from Fick models incorporating cerebral oxygen extraction fraction and cerebral blood flow. Hypercapnia also results in oxidation of cytochromecoxidase, complex IV of the mitochondrial respiratory chain, implicating a change in cellular metabolism. The aim of this study was to combine systems modelling with non-invasive measurements of cerebral tissue oxygenation, cerebral blood flow, and cytochromecoxidase redox state to evaluate any metabolic effects of hypercapnia. Cerebral tissue oxygen saturation and cytochrome oxidase redox state were measured with broadband near infrared spectroscopy and cerebral blood flow velocity using transcranial Doppler ultrasound. Data collected during 5-minutes hypercapnia in human volunteers were analyzed using a Fick model to determine changes in brain oxygen consumption and a mathematical model of cerebral hemodynamics and metabolism (BrainSignals) to inform on the potential mechanisms of any observed changes. Systemic physiology - blood pressure, arterial oxygen saturations and end-tidal carbon dioxide - served as model inputs. The extent of the hypercapnic oxidation of cytochrome oxidase required modifications of the BrainSignals model; simulations compared two possible modifications that could cause this oxidation - adecreasein metabolic substrate supply or anincreasein metabolic demand. Only the decrease in substrate supply was able to explain both the enzyme redox state changes and the Fick calculated drop in brain oxygen consumption. These modelled outputs are consistent with, but do not prove, previous reports of CO2inhibition of succinate dehydrogenase, complex II of the mitochondrial respiratory chain. These findings suggest that hypercapnia may have physiologically significant effects suppressing oxidative metabolism in humans and perturbing mitochondrial signaling pathways in health and disease.
Nonlinear fusion is optimal for a wide class of multisensory tasks
Authors: Ghosh Marcus , Béna Gabriel , Bormuth Volker , Goodman Dan F. M.
Published: July 2023

Animals continuously detect information via multiple sensory channels, like vision and hearing, and integrate these signals to realise faster and more accurate decisions; a fundamental neural computation known as multisensory integration. A widespread view of this process is that multimodal neurons linearly fuse information across sensory channels. However, does linear fusion generalise beyond the classical tasks used to explore multisensory integration? Here, we develop novel multisensory tasks, which focus on the underlying statistical relationships between channels, and deploy models at three levels of abstraction: from probabilistic ideal observers to artificial and spiking neural networks. Using these models, we demonstrate that when information provided by different channels is not independent, linear fusion performs sub-optimally and even fails in extreme cases. This leads us to propose a simple nonlinear algorithm for multisensory integration which is compatible with our current knowledge of multimodal circuits, excels in naturalistic settings and is optimal for a wide class of multisensory tasks. Thus, our work emphasises the role of nonlinear fusion in multisensory integration, and provides testable hypotheses for the field to explore at multiple levels: from single neurons to behaviour.

Key Points

We introduce a novel set of tasks, based on comodulating the signals from multiple channels.

We show that linear fusion performs sub-optimally on these tasks and even fails in extreme cases.

In contrast,nonlinear fusionis optimal and excels in naturalistic settings, like predator-prey interactions.

We demonstrate that networks of spiking neurons approximate the behaviour of this nonlinear algorithm, when trained on these tasks.

Finally, we explore how single neuron properties allow networks to approximate nonlinear fusion.
Estimating foraging behavior in rodents using a modified paradigm measuring threat imminence dynamics
Authors: Meng Xianzong , Chen Ping , Veltien Andor , Palavra Tony , Veld Sjors In’t , Grandjean Joanes , Homberg Judith R
Published: July 2023

Animals display defensive behaviors in response to threats to avoid danger and approach rewards. In nature, these responses did not evolve alone but are always accompanied by motivational conflict. A semi-naturalistic threat imminence continuum model models the approach-avoidance conflict and is able to integrate multiple defensive behaviors into a single paradigm. However, its comprehensive application is hampered by the lack of a detailed protocol and data about some fundamental factors including sex, age, and motivational level. Here, we modified a previously established paradigm measuring threat imminence continuum dynamics, involving modifications of training and testing protocols, and utilization of commercial materials combined with open science codes, making it more standardized and easier to replicate. We demonstrate that foraging behavior is modulated by age, hunger level, and sex. This paradigm can be used to study defensive behaviors in animals in a more naturalistic manner with relevance to human approach-avoid conflicts and associated psychopathologies.

Highlights

We provide detailed guidance for setting up a modified paradigm for the threat imminence continuum model with commercial materials and open-source codes.

We propose a modified paradigm for the threat imminence continuum model to quantify foraging behaviors.

Our method enables comparison between groups as a function of multiple factors including age and food restriction.

Graphic Summary
A host shift as the origin of tomato bacterial canker caused byClavibacter michiganensis
Authors: Yañez-Olvera Alan G. , Gómez-Díaz Ámbar G. , Selem-Mojica Nelly , Rodríguez-Orduña Lorena , Lara-Ávila José Pablo , Varni Vanina , Alcoba Florencia , Croce Valentina , Siri María Inés ,   Clavibacter Consortium, Barona-Gómez Francisco
Published: July 2023

Clavibacter, a plant endophytic actinobacterial genus, includes phytopathogens with devasting effects on several crops.C. michiganensis, the seed-borne and causal agent of bacterial canker in tomato, is arguably the most notorious species of the genus. Yet, its origin and natural reservoirs remain elusive. Moreover,C. michiganensispopulations show different genetic pathogenicity profiles with equally unpredictable plant disease outcomes. To tackle these uncertainties, here we analyze genomic data generated during a decade-long survey ofClavibacterin wild and commercial tomato cultivars, providing evolutionary insights that informed on the pathogenicity of this phytopathogen. Unexpectedly, our phylogeny situate the last common ancestor ofC. michiganensisnext toClavibacterisolates from grasses rather than to the sole strain we could isolate from wild tomato, which is closer toC. capsiciassociated with pepper. Pathogenicity profiling of selectedC. michiganensisisolates, together withC. phaseoliandC. californiensisas sister taxa of the grass clade, and the newly isolatedC. capsicifrom wild tomato, was found to be congruent with the proposed phylogenetic relationships. Furthermore, we identified gene enrichment after an evolutionary bottleneck leading to the appearance ofC. michiganesis, including known pathogenicity factors but also hitherto unnoticed genes with such potential,i.e.,nutrient acquisition and specialized metabolite metabolic gene clusters. The holistic perspective provided by our long-term and in-depth analyses hints towards a host shift event as the origin of the causative agent of bacterial canker in tomato, leading to a complex ofC. michiganensiswith pathogenicity factors that remain to be characterized.
Detecting, mapping, and suppressing the spread of a decade-longPseudomonas aeruginosanosocomial outbreak with genomics
Authors: Stribling William , Hall Lindsey R. , Powell Aubrey , Harless Casey , Martin Melissa J. , Corey Brendan W. , Snesrud Erik , Ong Ana , Maybank Rosslyn , Stam Jason , Bartlett Katie , Jones Brendan T. , Preston Lan N. , Lane Katherine F. , Thompson Bernadette , Young Lynn M. , Kwak Yoon I. , Barsoumian Alice E. , Markelz Ana-Elizabeth , Kiley John L. , Cybulski Robert J. , Bennett Jason W. , Mc Gann Patrick T. , Lebreton Francois
Published: July 2023

Whole-genome sequencing is revolutionizing bacterial outbreak investigation but its application to the clinic remains limited. In 2020, prospective and retrospective surveillance detected aPseudomonas aeruginosaoutbreak with 254 isolates collected from 82 patients in 27 wards of a hospital. Its origin was dated to the late 90s, just after the facility opened, and patient-to-patient and environment-to-patient cases of transmission were inferred. Over time, two epidemic subclones evolved in separate hosts and hospital areas, including newly opened wards, and hospital-wide sampling confirmed reservoirs persisted in the plumbing. Pathoadaptive mutations in genes associated with virulence, cell wall biogenesis, and antibiotic resistance were identified. While the latter correlated with the acquisition of phenotypic resistances to 1st (cephalosporin), 2nd (carbapenems) and 3rd (colistin) lines of treatment, maximum parsimony suggested that a truncation in a lipopolysaccharide component coincided with the emergence of a subclone prevalent in chronic infections. Since initial identification, extensive infection control efforts guided by routine, near real-time surveillance have proved successful at slowing transmission.

SIGNIFICANCE STATEMENT

Every year, millions of hospital-associated infections are threatening patient lives. This, in a world in which rates of resistances to existing antibiotics are increasing. And this, at a time dubbed the post-antibiotic era when new drugs are scarce. But now is also the golden age of genomics. Here, applying this transformative technology to the clinic revealed an outbreak ofPseudomonas aeruginosa, resistant to last line antibiotics, that had escaped detection for decades. The mapping of transmission chains, through hospital floors, pointed to environmental reservoirs in intensive care units but also provided critical insights into the evolution and adaptation of this pathogen. Genomic data, shared in near real-time with the hospital, resulted in targeted interventions and the prevention of new cases.
Structural Coverage of the Human Interactome
Authors: Kosoglu Kayra , Aydin Zeynep , Tuncbag Nurcan , Gursoy Attila , Keskin Ozlem
Published: July 2023

Complex biological processes in cells are embedded in the interactome, representing the complete set of protein-protein interactions. Mapping and analyzing the protein structures are essential to fully comprehending these processes’ molecular details. Therefore, knowing the structural coverage of the interactome is essential to show the current limitations. Structural modeling of protein-protein interactions requires accurate protein structures. In this study, we mapped all experimental structures to the reference human proteome. Later, we found the enrichment in structural coverage when complementary methods such as homology modeling and deep learning (AlphaFold) are included. We then collected the interactions from the literature and databases to form the reference human interactome resulting in 117,897 non-redundant interactions. When we analyzed the structural coverage of the interactome, we found that the number of experimentally determined protein complex structures is scarce, corresponding to 3.95% of all binary interactions. We also analyzed known and modeled structures to potentially construct the structural interactome with a docking method. Our analysis showed that 12.97% of the interactions from HuRI, 73.62%, and 32.94% from the filtered versions of STRING and HIPPIE could potentially be modeled with a high structural coverage or accuracy, respectively. Overall, this paper provides an overview of the current state of structural coverage of the human proteome and interactome.

Significance Statement

We gathered binary protein-protein interactions from three prominent interactome databases to create a comprehensive human reference interactome. We quantified the structural coverage of the human interactome using already available structural data from four different sources. We further evaluate the percentage of interactions that can be accurately predicted using docking methods.
ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole genome sequencing data
Authors: Calendo Gennaro , Kusic Dara , Madzo Jozef , Gharani Neda , Scheinfeldt Laura
Published: July 2023

Long-read sequencing technologies offer new opportunities to generate high confidence phased whole genome sequencing data for robust pharmacogenetic annotation. Here we describe a new user-friendly R package, ursaPGx, designed to accept multi-sample phased whole genome sequencing data VCF input files and output star allele annotations for pharmacogenes annotated in PharmVar.
Investigating the basis of lineage decisions and developmental trajectories in the dorsal spinal cord through pseudotime analyses
Authors: Gupta Sandeep , Heinrichs Eric , Novitch Bennett G. , Butler Samantha J.
Published: July 2023

Dorsal interneurons (dIs) in the spinal cord encode the perception of touch, pain, heat, itch, and proprioception. While previous studies using genetic strategies in animal models have revealed important insights into dI development, the molecular details by which dIs arise as distinct populations of neurons remain incomplete. We have developed a resource to investigate dI fate specification by combining a single-cell RNA-Seq atlas of mouse ESC-derived dIs with pseudotime analyses. To validate thisin silicoresource as a useful tool, we used it to first identify novel genes that are candidates for directing the transition states that lead to distinct dI lineage trajectories, and then validated them usingin situhybridization analyses in the developing mouse spinal cordin vivo. We have also identified a novel endpoint of the dI5 lineage trajectory and found that dIs become more transcriptionally homogenous during terminal differentiation. Together, this study introduces a valuable tool for further discovery about the timing of gene expression during dI differentiation and demonstrates its utility clarifying dI lineage relationships.

Summary statement

Pseudotime analyses of embryonic stem cell-derived dorsal spinal interneurons reveals both novel regulators and lineage relationships between different interneuron populations.
Exome capture of Antarctic krill (Euphausia superba) for cost effective population genetics of historical collections
Authors: White Oliver , Tarling Geraint , Hughes Lauren , Walkington Sarah , Clark Matt
Published: July 2023

Antarctic Krill (Euphausia superba) is a pivotal keystone species in the Southern Ocean ecosystem, with immense ecological and commercial significance. However, its vulnerability to climate change necessitates urgent investigation of its population genetics and adaptive responses. Historical spirit collections of Antarctic krill from the early 20th century represent an ideal opportunity for genomic research, to investigate how krill have changed over time and been impacted by predation, fishing and climate change. In this study, we assessed the utility of shotgun sequencing and exome capture for genomic analyses with historical spirit collections of Antarctic krill. Because the krill genome is very large (48Gb) two full-length transcriptomes were generated and used to identify putative targets for targeted resequencing. Skim genome sequencing allowed sample and library quality control. By comparing genome to exome resequencing of the same libraries we calculate enrichment and variant calling metrics. Full-length mitochondrial and nuclear ribosomal sequences were successfully assembled from genomic data demonstrating that endogenous DNA sequences could be assembled from historical collections. We find that exome capture provided enrichment of on-target sequence data, with increased depth and higher variant quality for targeted loci. Our findings demonstrate the feasibility of extracting genomic information from historical krill samples, despite the challenges of fragmented DNA and huge genome size unlocking such collections to provide valuable insights into past and present krill diversity, resilience, and adaptability to climate change. This approach unlocks the potential for broader genomic studies in similar samples, and for enhancing conservation efforts and fisheries management in the Southern Ocean ecosystem.
Direct and culture-independent detection of low-abundantClostridioides difficilein environmental DNA via PCR
Authors: Schüler Miriam A. , Schneider Dominik , Poehlein Anja , Daniel Rolf
Published: July 2023

Clostridioides difficilerepresents a major burden to public health. As a well-known nosocomial pathogen whose occurrence is highly associated with antibiotic treatment, most examinedC. difficilestrains originated from clinical specimen and were isolated under selective conditions emplyoing antibiotics. This suggests a significant bias among analysedC. difficilestrains, which impedes a holistic view on this pathogen. In order to support extensive isolation ofC. difficilestrains from environmental samples, we designed a detection PCR that targets thehpdBCAoperon and thereby identifies low abundances ofC. difficilein environmental samples. Amplicon-based analyses of diverse environmental samples demonstrated that the designed PCR is highly specific forC. difficileand successfully detectedC. difficiledespite its absence in general 16S rRNA gene-based detection strategies. Further analyses revealed the potential of thehpdBCAdetection PCR sequence for initial phylogenetic classification, which allows assessingC. difficilediversity in environmental samples via amplicon sequencing. Our findings furthermore showed thatC. difficilestrains isolated under antibiotic treatment from environmental samples were originally dominated by other strains according to detection PCR amplicon results. This provided evidence for selective cultivation of under-represented but antibiotic-resistant isolates. Thereby, we revealed a substantial bias inC. difficileisolation and research.

Importance

Clostridioides difficileis mainly responsible for hospital-acquired infections after antibiotic treatment with serious morbidity and mortality worldwide. Research on this pathogen and its virulence focused on bacterial isolation from clinical specimen under antibiotic treatment, which implies a substantial bias in isolated strains. Comprehensive studies however require an unbiased strain collection, which is accomplished by isolation ofC. difficilefrom diverse environmental samples and avoiding antibiotic-based enrichment strategies. Thus, isolation can significantly benefit from ourC. difficile-specific detection PCR, which rapidly verifiesC. difficilepresence in environmental samples and further allows estimation of theC. difficilediversity by using NGS.
Does soil history decline in influencing the structure of bacterial communities ofBrassica napushost plants across different growth stages?
Authors: Blakney Andrew J.C. , St-Arnaud Marc , Hijri Mohamed
Published: July 2023

Soil history has been shown to condition future plant-soil microbial communities up to a year after being established. However, previous experiments have also illustrated that mature, adult plants can “re-write”, or mask, different soil histories through host plant-soil microbial community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Therefore, in this experiment we tested the hypothesis that previously established soil histories will decrease in influencing the structure ofBrassica napusbacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B.napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere and roots ofB.napusat different growth stages— the initial seeding conditions, seedling, rosette, bolting, and flower— from all three soil history plots. We compared the taxonomic composition and diversity of bacterial communities, as estimated using 16S rRNA metabarcoding, to identify any changes associated with soil history and growth stages on the differentB. napussoil bacterial communities. We found that soil history remained significant across each growth stage in structuring the bulk soil and rhizosphere communities, but not the roots. This suggests that the host plant’s capacity to “re-write” different soil histories may be quite limited as key components that constitute the soil history’s identity remain present and continue to impact bacterial communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.
Smart Leginon enables cryoEM screening automation across multiple grids
Authors: Sawh-Gopal Anjelique , Ishemgulova Aygul , Chua Eugene Y.D. , Aragon Mahira F. , Mendez Joshua H. , Eng Edward T. , Noble Alex J.
Published: July 2023

CryoEM multi-grid screening is often a tedious process that demands hours of attention. Here, this protocol shows how to set up standardLeginoncollection andSmart Leginon Autoscreento automate this process. This protocol can be applied to the majority of cryoEM holey foil grids.

Advancements in cryo-electron microscopy (cryoEM) techniques over the past decade have allowed structural biologists to routinely resolve macromolecular protein complexes to near-atomic resolution. The general workflow of the entire cryoEM pipeline involves iterating between sample preparation, cryoEM grid preparation, and sample/grid screening before moving on to high-resolution data collection. Iterating between sample/grid preparation and screening is typically a major bottleneck for researchers, as every iterative experiment must optimize for sample concentration, buffer conditions, grid material, grid hole size, ice thickness, and protein particle behavior in the ice, amongst other variables. Furthermore, once these variables are satisfactorily determined, grids prepared under identical conditions vary widely in whether they are ready for data collection, so additional screening sessions prior to selecting optimal grids for high-resolution data collection are recommended. This sample/grid preparation and screening process often consumes several dozen grids and days of operator time at the microscope. Furthermore, the screening process is limited to operator/microscope availability and microscope accessibility. Here, we demonstrate how to useLeginonandSmart Leginon Autoscreento automate the majority of cryoEM grid screening.Autoscreencombines machine learning, computer vision algorithms, and microscope-handling algorithms to remove the need for constant manual operator input.Autoscreencan autonomously load and image grids with multi-scale imaging using an automated specimen-exchange cassette system, resulting in unattended grid screening for an entire cassette. As a result, operator time for screening 12 grids may be reduced to ∼10 minutes withAutoscreencompared to ∼6 hours using previous methods which are hampered by their inability to account for high variability between grids. This protocol and video tutorial first introduces basicLeginonsetup and functionality, then demonstratesAutoscreenfunctionality step-by-step from the creation of a template session to the end of a 12 grid automated screening session.
Improving healthcare team harmony through collaborative team reflection and mindfulness
Authors: Kang Matthew JY , Aung Ar Kar , Gibbs Jo , Gibbs Harry
Published: July 2023

Hospital wards, staffed by the multidisciplinary team, are complex environments where teamwork, communication and psychological safety is essential for coordinated care delivery, yet are faced with challenges such as staffing changes and complex care needs. However, there is little literature on interventions to assist staff connect as a team. We evaluated a brief daily group based on team reflection and mindfulness aimed at a multidisciplinary general medicine team, using measures of team functioning (effectiveness, communication, and psychological safety).

We found that participants reported significant improvement in the meeting’s effectiveness (U=184, p=0.013), team morale (U=123, p<0.001), and focus (U=183, p<0.001) after the program’s commencement. Furthermore, participants who attended the program for at least a week reported they felt more psychologically safe (U=116, p=0.032). We also found significant positive correlation between measures of team functioning and the number of sessions they attended the program (effectiveness of the interdisciplinary meeting r=0.509, p<0.001; team’s communication and functioning (r=0.509, p<0.001). The post-intervention focus group highlighted the program helped build relationships within the team, improve psychological safety, and subsequently shifted the team’s behaviour to be more supportive of the overall team. Our program improved the functioning of a multidisciplinary healthcare team, with the overall aim to deliver better patient care.
Community structure of known and previously unknown endobacteria associated with spores of arbuscular mycorrhizal fungi
Authors: Lastovetsky Olga A. , Caruso Tancredi , Brennan Fiona P. , Wall David , Pylni Susanna , Doyle Evelyn
Published: July 2023

Arbuscular mycorrhizal fungi (AMF) are ubiquitous plant root symbionts which can house two endobacteria:Ca.Moeniiplasma glomeromycotorum (CaMg) andCa. Glomeribacter gigasporarum (CaGg). However, little is known about their distribution and population structure in natural AMF populations and whether AMF can harbour other endobacteria. We isolated AMF from two environments and surveyed the surface-sterilized spores for endobacteria. We found thatCaMg andCaGg differed significantly in distribution wherebyCaMg were extremely abundant (80%) andCaGg were extremely rare (2%) in both environments. Unexpectedly, we discovered an additional and previously unknown level of bacterial diversity within AMF spores which extended beyond the known endosymbionts, with as many as 277 other bacterial taxa detected in individual spores. Detailed analysis of endobacterial communities inside AMF spores revealed that: (i)CaGg were not limited in distribution to theGigasporaceafamily of AMF, as previously thought, (ii)CaMg community structure was driven by AMF host genotype, (iii) a significant inverse correlation existed between the diversity ofCaMg and diversity of all other endobacteria. The latter suggests the existence of competition dynamics between different bacterial populations inside AMF spores and provides a basis for generation of testable hypotheses regarding the function ofCaMg in AMF biology.
CURTAIN – A Unique Web-based tool for exploration and sharing of MS-based proteomics data
Authors: Phung Toan K. , Berndsen Kerryn , Phan Tran Le Cong Huyen Bao , Muqit Miratul M. K. , Alessi Dario R. , Nirujogi Raja S.
Published: July 2023

To facilitate analysis and sharing of mass spectrometry (MS)-based proteomics data we created tools called CURTAIN (https://curtain.proteo.info) and CURTAIN-PTM (https://curtainptm.proteo.info). These enable the non-MS expert to interactively peruse volcano plots; deconvolute primary experimental data to individual replicates that can be visualized in bar charts or violin plots allowing statistical analysis; and export of plots in SVG format. They also permit assessment of experimental quality by correlation matrix and profile plot. Within CURTAIN, the user can analyze domain structure, AlphaFold predicted structure, reported interactors, relative expression, disease and pharmaceutical links, and mutagenesis information on all selected hits. Moreover, CURTAIN-PTM permits the comparison of all identified PTM sites on protein(s) of interest with PTM information contained within selected databases. For phosphorylation site analysis CURTAIN-PTM links with the kinase library to predict upstream kinases that phosphorylate sites of interest. We provide examples of the utility of CURTAIN and CURTAIN-PTM in analyzing how targeted degradation of the PPM1H Rab phosphatase that counteracts the Parkinson’s LRRK2 kinase impacts cellular protein levels and phosphorylation sites. We reanalyzed a ubiquitylation dataset, characterizing the PINK1-Parkin pathway activation in primary neurons, revealing new data of interest not highlighted previously. CURTAIN and CURTAIN-PTM are free to use and open-source and will enable researchers to share and maximize the analysis and impact of their proteomics data. We advocate that differential expression proteomic data should be published containing a shareable CURTAIN web-link, allowing readers to better explore their data.

Significance Statement

To enable non-experts to better share and explore mass spectrometry data, we have generated using open-source software, interactive tools termed CURTAIN and CURTAIN-PTM. These tools enable users’ to save their analysis sessions with a sharable unique web-link, enabling other researchers to visualize and further analyze these datasets. These links can also be reported in publications allowing readers to further survey the reported data. We discuss benefits for the research community of publishing proteomic data containing a shareable web-link.
Lariat debranching by RNA DEBRANCHING ENZYME 1 depends on SICKLE inArabidopsis thaliana
Authors: Kovak Emma E. , Marshall Carine M. , Molinari Mayla D. C. , Nepomuceno Alexandre L. , Harmon Frank G.
Published: July 2023

Spliceosome mediated intron removal from precursor mRNAs (pre-mRNAs) generates circular RNAs called intron lariats. RNA DEBRANCHING ENZYME 1 (DBR1) ribonucleases linearize, or debranch, intron lariats to allow their degradation.DBR1genes occur across eukaryotes and are essential in animals and plants. High levels of intron lariats in the weakArabidopsis thaliana dbr1-2allele inhibits primary microRNA (pri-miRNA) processing, disrupting miRNA production and miRNA-regulated growth and development. Arabidopsissickle(sic) mutants alter pri-miRNA processing and pre-mRNA splicing. This study demonstratessicmutants accumulate intron lariats matching those in weakdbralleles. The strongsic-1and weakdbr1-3alleles together cause synthetic lethality, while weaksic-3withdbr1-3has intron lariat accumulation likesic-3. Further,sic-3,dbr1-3, andsic-3 dbr1-3similarly alter circadian rhythms and growth of roots and rosettes. The conserved MPLKIP amino acid motif in SIC mediates physical interaction with DBR1in vitroand is required for intron lariat debranchingin vivo. Thus, MPLKIP containing proteins, like SIC and human TTDN1, act with cognate DBR1 proteins to maintain RNA homeostasis critical for growth and development.
VCF1 is an unconventional p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates
Authors: Mirsanaye Ann Schirin , Hoffmann Saskia , Weisser Melanie , Mund Andreas , Mendez Blanca Lopez , Typas Dimitris , van den Boom Johannes , Benedict Bente , Hendriks Ivo A. , Nielsen Michael Lund , Meyer Hemmo , Duxin Julien P. , Montoya Guillermo , Mailand Niels
Published: July 2023

The hexameric AAA+ ATPase p97/VCP functions as an essential mediator of ubiquitin-dependent cellular processes, extracting ubiquitylated proteins from macromolecular complexes or membranes by catalyzing their unfolding. p97 is directed to ubiquitylated client proteins via multiple cofactors, most of which interact with the p97 N-domain. Here, we discovered that FAM104A, a protein of unknown function that we named VCF1 (VCP/p97 Cofactor FAM104 1), acts as a novel p97 cofactor in human cells. Detailed structure-function studies revealed that VCF1 directly binds p97 via a conserved novel α-helical motif that recognizes the p97 N-domain with unusually high affinity, exceeding that of other cofactors. We show that VCF1 engages in joint p97 complex formation with the heterodimeric primary p97 cofactor UFD1-NPL4 and promotes p97-UFD1-NPL4-dependent proteasomal degradation of ubiquitylated substrates in cells. Mechanistically, VCF1 indirectly stimulates UFD1-NPL4 interactions with ubiquitin conjugates via its binding to p97 but has no intrinsic affinity for ubiquitin. Collectively, our findings establish VCF1 as an unconventional p97 cofactor that promotes p97-dependent protein turnover by facilitating p97-UFD1-NPL4 recruitment to ubiquitylated targets.
Occurrence ofAmaranthus palmeriin Israeli agriculture: status of spread and response to glyphosate and trifloxysulfuron
Authors: Abu-Nassar Jackline , Wallach Amit , Winkler Eilon , Eizenberg Hanan , Matzrafi Maor
Published: July 2023

Amaranthus palmeriS. Watson is a dioecious annual weed species, originating from the Southern USA, spreading rapidly beyond its original range into Europe and the Mediterranean region. In Israel,A. palmeridistribution has expanded quickly in recent years, with farmers reporting on weed control failure using acetolactate synthase (ALS) inhibitors. Furthermore, recent studies have documented glyphosate-resistant cases from other countries in the region, such as Spain, Greece, and Turkey. We conducted a survey in order to understandA. palmeridistribution and study the occurrence of herbicide resistance to both glyphosate and trifloxysulfuron in different fields across the country. According to our data,A. palmeripopulation locations are aligned with the major agricultural areas for summer field crops, including the Hula Valley, Jezreel Valley, and the Southern Coastal Plain. Regarding herbicide responses, while several populations showed a reduced response to glyphosate, dose-response assays did not show resistance to the recommended labeled field rate. For the ALS inhibitor trifloxysulfuron, the proportion of resistant individuals was very high, especially in the southern coastline region, with an R-value of 0.77. Four populations used for dose-response studies were highly resistant, surviving at four times the recommended labeled field rate of trifloxysulfuron (30 g a.i. ha-1). Sequencing of the ALS gene, Trp574 to Leu alteration in resistant populations was recorded. The high level of resistance observed in this study, alongside the target-site mutation found in populations ofA. palmeri, endangers the future use of ALS inhibitors in corn, cotton, and other summer crops grown in Israel.
FAM104 proteins promote the nuclear localization of p97/VCP
Authors: Körner Maria , Meyer Susanne , Marincola Gabriella , Kern Maximilian , Grimm Clemens , Schülein-Völk Christina , Fischer Utz , Hofmann Kay , Buchberger Alexander
Published: July 2023

The ATPase p97 (also known as VCP, Cdc48) has crucial functions in a variety of important cellular processes such as protein quality control, organellar homeostasis and DNA damage repair, and its de-regulation is linked to neuro-muscular diseases and cancer. p97 is tightly controlled by numerous regulatory cofactors, but the full range and function of the p97–cofactor network is unknown. Here, we identify the hitherto uncharacterized FAM104 proteins as a conserved family of p97 interactors. FAM104 proteins bind p97 directlyviaa novel, alpha-helical motif and associate with the p97- UFD1-NPL4 complex in cells. FAM104 proteins localize to the nucleus and promote both the nuclear import and chromatin binding of p97. Loss of FAM104 proteins results in slow growth and hypersensitivity to p97 inhibition in the absence and presence of DNA damage, suggesting that FAM104 proteins are critical regulators of nuclear p97 functions.
Shared Structural Features of Miro Binding Control Mitochondrial Homeostasis
Authors: Covill-Cooke Christian , Kwizera Brian , López-Doménech Guillermo , Thompson Caleb O.D. , Cheung Ngaam J. , Cerezo Ema , Peterka Martin , Kittler Josef T. , Kornmann Benoît
Published: July 2023

Miro proteins are universally conserved mitochondrial calcium-binding GTPases that regulate a multitude of mitochondrial processes, including transport, clearance and lipid trafficking. Miro binds a variety of client proteins involved in these functions. How this binding is operated at the molecular level and whether and how it is important for mitochondrial health, however, remains unknown. Here, we show that known Miro clients all use a similar short motif to bind the same structural element: a highly conserved hydrophobic pocket in the calcium-binding domain of Miro. Using these Miro-binding motifs, we identified direct interactorsde novo, including yeast Mdm34, and mammalian MTFR1/2/1L, VPS13D and Parkin. Given the shared binding mechanism and conservation across eukaryotes, we propose that Miro is a universal mitochondrial adaptor coordinating mitochondrial health.

One-Sentence Summary

Functionally diverse mitochondrial proteins interact with a conserved hydrophobic pocket on the calcium-binding Miro-GTPases.
Variation in the Microbiomes of the Basidiomycete FungiScleroderma citrinum(Pers.) andPisolithus arhizus(Pers.): a tale of two saprotrophs
Authors: Cullings Ken , Bhardwaj Shilpa R. , Spector Michael
Published: July 2023

In this study we used high throughput DNA sequencing and ICP-MS to compare the microbiome of the common earthball fungus,Scleroderma citrinum(Pers.) to that of its sister taxon in the Sclerodermataceae,Pisolithus arhizus(Scop.). ICP-MS analysis demonstrates thatS. citrinumis enriched in silica, sulfur and zinc relative toP. arhizus, whileP. arhizusis enriched in arsenic, calcium, cadmium, cobalt, copper, lithium, magnesium, molybdenum, nickel, potassium and vanadium. Statistical analysis of molecular data indicates that the microbiome ofP. arhizusis both richer and more diverse than that ofS. citrinum, and that the microbiomes are significantly different with that ofS. citrinumbeing enriched in Cyanobacteria represented by the chloroplast of a photosynthetic, cryptoendolithic red alga, Saccharibacteria (TM-7), and Planctomycetes, while that ofP. arhizusis enriched in Gemmatimonadetes, Latescibacteria, Elusomicrobia, and Tectomicrobia. Further, theP. arhizusmicrobiome is enriched in anaerobes relatives to that ofS. citrinum, probably reflecting anaerobic zones previously measured inP. arhizus. Together, the data indicate diverse microbiomes comprised of aromatic hydrocarbon-degrading, metal- and radiotolerant bacteria, indicating that these fungi may provide a rich source of novel microbes suitable for bioremediation strategies.
CRUX, a platform for visualising, exploring and analysing cancer genome cohort data
Authors: El-Kamand Sam , Quinn Julian M.W. , Sareen Heena , Becker Therese M. , Wong-Erasmus Marie , Cowley Mark J.
Published: July 2023

To better understand how tumours develop, identify prognostic biomarkers, and find new treatments, researchers have generated vast catalogues of cancer genome data. However, these datasets are complex so interpreting their important features requires specialized computational skills and analytical tools, which presents a significant technical challenge. To address this, we developed CRUX, a platform for exploring genomic data from cancer cohorts. CRUX enables researchers to perform common analyses including cohort comparisons, biomarker discovery, survival analysis, and create visualisations including oncoplots and lollipop charts. CRUX simplifies cancer genome analysis in several ways: (1) it has an easy-to-use graphical interface; (2) it enables users to create custom cohorts, as well as analyse precompiled public and private user-created datasets; (3) it allows analyses to be run locally to address data privacy concerns (though an online version is also available); and (4) it makes it easy to use additional specialized tools by exporting data in the correct formats. We showcase CRUX’s capabilities with case studies employing different types of cancer genome analysis, demonstrating how it can be used flexibly to generate valuable insights into cancer biology. CRUX is freely available athttps://github.com/CCICB/CRUXandhttps://ccicb.shinyapps.io/crux(DOI: 10.5281/zenodo.8015714).
Regulation of late-acting operons by three transcription factors and a CRISPR-Cas component duringMyxococcus xanthusdevelopment
Authors: Saha Shreya , Kroos Lee
Published: July 2023

Upon starvation rod-shapedMyxococcus xanthusbacteria form mounds and then differentiate into round stress-resistant spores. Little is known about the regulation of late-acting operons important for spore formation. C-signaling has been proposed to activate FruA, which binds DNA cooperatively with MrpC to increase transcription of many genes. We report that this model can explain regulation of thefadIJoperon involved in spore metabolism, but not that of the spore coat biogenesis operonsexoA-I,exoL-P, andnfsA-H. Rather, a mutation infruAincreased the transcript levels from these operons early in development, suggesting negative regulation by FruA initially, and a mutation inmrpCaffected transcript levels from each operon differently. FruA bound to all four promoter regionsin vitro, but strikingly each promoter region was unique in terms of whether or not MrpC and the DNA-binding domain of Nla6 bound, and in terms of cooperative binding. Furthermore, the DevI component of a CRISPR-Cas system is a negative regulator of all four operons, based on transcript measurements. Our results demonstrate complex regulation of sporulation genes by three transcription factors and a CRISPR-Cas component, which we propose thwarts viral intrusion while making spores suited to withstand starvation and environmental insults.
MRC2020: improvements to Ximdisp and the MRC image-processing programs
Authors: Short J. M. , Palmer C. M. , Burnley T. , Winn M. D. , Zhang Q. , Venkataram Prasad B. V. , Chen S. , Crowther R. A. , Unwin P. N. T. , Henderson R.
Published: July 2023

The great success of single-particle electron cryo-microscopy (cryoEM) during the last decade has involved the development of powerful new computer programs and packages that guide the user along a recommended processing workflow, in which the wisdom and choices made by the developers help everyone, especially new users, to obtain excellent results. The ability to carry out novel, non-standard or unusual combinations of image-processing steps is sometimes compromised by the convenience of a standard procedure. Some of the older programs were written with great flexibility and are still very valuable. Among these, the original MRC image-processing programs for structure determination by 2D crystal and helical processing alongside general-purpose utility programs such as Ximdisp, label, imedit and twofile are still available. This work describes an updated version of the MRC software package (MRC2020) that is freely available from CCP-EM. It includes new features and improvements such as extensions to the MRC format that retain the versatility of the package and make it particularly useful for testing novel computational procedures in cryoEM.