bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Mapping of Keratin Networks in 3D
Authors: Windoffer Reinhard , Schwarz Nicole , Yoon Sungjun , Piskova Teodora , Scholkemper Michael , Stegmaier Johannes , Bönsch Andrea , Di Russo Jacopo , Leube Rudolf E.
Published: December 2021

Mechanobiology requires precise quantitative information on processes taking place in specific 3D microenvironments. Connecting the abundance of microscopical, molecular, biochemical and cell mechanical data with defined topologies has turned out to be extremely difficult. Establishing such structural and functional 3D maps needed for biophysical modeling is a particular challenge for the cytoskeleton, which consists of long and interwoven filamentous polymers coordinating subcellular processes and interactions of cells with their environment. To date, useful tools are available for the segmentation and modeling of actin filaments and microtubules but comprehensive tools for the mapping of intermediate filament organization are still lacking. In this work, we describe a workflow to model and examine the complete 3D arrangement of the keratin intermediate filament cytoskeleton in epithelial cells both in vitro and in vivo. Numerical models are derived from super resolution 3D imaging of fluorescence-tagged keratin filaments. They are interrogated and annotated at different length scales using different modes of visualization including immersive virtual reality. In this way, information is provided on network organization at the subcellular level including mesh arrangement, density and isotropic configuration as well as details on filament morphology such as bundling, curvature and orientation. We show that the comparison of these parameters helps to identify, in quantitative terms, similarities and differences of keratin network organization in epithelial cell types defining subcellular domains, notably basal, apical, lateral and perinuclear systems. The described approach and the presented data are pivotal for generating mechanobiological models that can be experimentally tested.
Root membrane ubiquitinome under short-term osmotic stress
Authors: Berger Nathalie , Demolombe Vincent , Hem Sonia , Rofidal Valérie , Steinmann Laura , Krouk Gabriel , Crabos Amandine , Nacry Philippe , Verdoucq Lionel , Santoni Véronique
Published: December 2021

Osmotic stress can be detrimental to plants, whose survival relies heavily on proteomic plasticity. Protein ubiquitination is a central post-translational modification in osmotic mediated stress. Plants use the ubiquitin (Ub) proteasome system to modulate protein content, and a role for Ub in mediating endocytosis and trafficking plant plasma membrane proteins has recently emerged. In this study, we used the K-ε-GG antibody enrichment method integrated with high-resolution mass spectrometry to compile a list of 719 ubiquitinated lysine (K-Ub) residues from 450 Arabidopsis root membrane proteins (58% of which are transmembrane proteins), thereby adding to the database of ubiquitinated substrates in plants. Although no Ub motifs could be identified, the presence of acidic residues close to K-Ub was revealed. Our ubiquitinome analysis pointed to a broad role of ubiquitination in the internalization and sorting of cargo proteins. Moreover, the simultaneous proteome and ubiquitinome quantification showed that ubiquitination is mostly not involved in membrane protein degradation in response to short osmotic treatment, but putatively in protein internalization as described for the aquaporin PIP2;1. Our in silico analysis of ubiquitinated proteins shows that two E2 Ub ligases, UBC32 and UBC34, putatively target membrane proteins under osmotic stress. Finally, we revealed a positive role for UBC32 and UBC34 in primary root growth under osmotic stress.
An effective workshop on “How to be an Effective Mentor for Underrepresented STEM Trainees”
Authors: Marshall Andrea G. , Palavicino-Maggio Caroline B. , Spencer Elsie , Vue Zer , Beasley Heather , Garza-Lopez Edgar , Brady Lillian , Conley Zachary , Neikirk Kit , Murray Sandra , Martinez Denise , Shuler Haysetta , Morton Derrick , Hinton Antentor
Published: December 2021

Despite an increase in programming to promote persons excluded by their ethnicity or race (PEER) scholars, minorities remain underrepresented in many STEM programs. The academic pipeline is largely leaky for underrepresented minority (URM) scholars due to a lack of effective mentorship. Many URM students experience microaggressions and discrimination from their mentors due to a lack of quality mentorship training. In this workshop, we provide a framework for how to be an effective mentor to URM trainees. Mentees, especially URM trainees, can flourish in effective mentoring environments where they feel welcomed and can comfortably develop new ideas without feeling threatened by external factors. Effective mentoring environments provide motivational support, empathy, cultural competency, and training.
Dynamic analysis and evaluation of asymptomatic infection in the spread of COVID-19
Authors: Xu Chuanqing , Zhang Zonghao , Huang Xiaotong , Cui Jingan
Published: December 2021

COVID-19 has spread worldwide for nearly two years. Many countries have experienced repeated epidemics, that is, after the epidemic has been controlled for a period of time, the number of new cases per day is low, and the outbreak will occur again a few months later. In order to study the relationship between this low level of infection and the number of asymptomatic infections, and to evaluate the role of asymptomatic infections in the development of the epidemic, we have established an improved infectious disease dynamics model that can be used to evaluate the spread of the COVID-19 epidemic, and fitted the epidemic data in the three flat periods in England. According to the obtained parameters, according to the calculation of the model, the proportion of asymptomatic infections in these three flat periods are 41%, 53% and 58% respectively. After the first flat period, the number of daily newly confirmed cases predicted by the model began to increase around July 1, 2020. After more than four months of epidemic spread, it reached a peak on November 12, which is consistent with the actual case situation. Unanimous. After the second flat period, the model predicts that the number of new confirmed cases per day will increase from about May 7, 2021, and after about 73 days of epidemic development, it will reach a peak on July 20, showing the overall trend of the epidemic. In the above, the predicted results of the model are consistent with the actual cases. After the third flat period, the number of daily newly diagnosed cases predicted by the model began to increase around December 1, 2021, and reached a peak in December, and the number of cases will drop to a very low level after May 2022. According to our research results, due to the large number of asymptomatic infections, the spread of the epidemic is not easy to stop completely in a short time. However, when the epidemic enters a period of flat time, nucleic acid testing is performed, and asymptomatic infections are isolated at home for 14 days (the recovery period of symptomatic infection is about 10 days) may be an option that can be considered to interrupt the transmission of the case.
Compromised CDK12 activity causes dependency on the non-essential spliceosome components
Authors: Pallasaho Satu , Gondane Aishwarya , Duveau Damien , Thomas Craig , Loda Massimo , Itkonen Harri M
Published: December 2021

Prostate cancer (PC) is the most common cancer in men and after development of the castration-resistant PC (CRPC), there are no curative treatment options. Inactivating mutations in cyclin-dependent kinase 12 (CDK12) define an aggressive sub-type of CRPC. We hypothesized that compromised CDK12 activity leads to significant rewiring of the CRPC cells, and that this rewiring results in actionable synthetic lethal interactions.

Methods

We used combinatorial lethal screening, ChIP-seq data, RNA-seq data, global alternative splicing analysis, and comprehensive mass spectrometry (MS) profiling to understand how the compromised CDK12 activity rewires the CRPC cells. In addition, we used DepMap-, PC- and CRPC-datasets as a strategy to identify factors that are selectively required by the CDK12-mutant cells.

Results

We show that inhibition of O-GlcNAc transferase (OGT) and CDK12 induces cancer cell-selective growth-defect. OGT catalyzes all nucleocytoplasmic O-GlcNAcylation, and we use unbiased MS-profiling to show that the short-term CDK12 inhibition induces hyper-O-GlcNAcylation of the spliceosome-machinery in PC and CRPC cells. Integration of DepMap- and a small scale-drug screen data reveled that depletion of CDK12 activity causes addiction to non-essential spliceosome components (CLK1/4 and SRPK1). CDK12-mutant tumors overexpress CLK1/4 and SRPK1. Finally, we show that the genomes of the CDK12-mutant tumors have lower DNA methylation, and that CDK12 inhibition induces the expression of the genes marked by DNA methylation.

Conclusions

Compromised CDK12 activity rewires DNA methylation, transcription and splicing, and this rewiring renders the affected cells addicted on the non-essential spliceosome components. We propose that inactivation of CDK12 is a biomarker for sensitivity against inhibitors of the non-essential spliceosome components just entering the clinical trials.

Abstract Figure
Semi-automated computational assessment of cancer organoid viability using rapid live-cell microscopy
Authors: Buehler Joseph D. , Bird Cylaina E. , Savani Milan R. , Gattie Lauren C. , Hicks William H. , Levitt Michael M. , Shami Mohamad El , Hatanpaa Kimmo J. , Richardson Timothy E. , McBrayer Samuel K. , Abdullah Kalil G.
Published: December 2021

The creation of patient-derived cancer organoids represents a key advance in preclinical modeling and has recently been applied to a variety of human solid tumor types. However, conventional methods used to assess cellular viability in tissue specimens are poorly suited for the evaluation of cancer organoids because they are time-intensive and involve tissue destruction. To address this issue, we established a suite of 3-dimensional patient-derived glioma organoids, treated them with chemoradiotherapy, stained organoids with non-toxic cell dyes, and imaged them using a rapid laser scanning confocal microscopy method termed “Apex Imaging”. We then developed and tested a fragmentation algorithm to quantify heterogeneity in the topography of the organoids as a potential surrogate marker of viability. This algorithm, SSDquant, provides a 3-dimensional visual representation of the organoid surface and a numerical measurement of the sum-squared distance (SSD) from the derived mass center of the organoid. We tested whether SSD scores correlate with traditional immunohistochemistry-derived cell viability markers (cellularity and cleaved caspase 3 expression) and observed statistically significant associations between them using linear regression analysis. Our work describes a quantitative, non-invasive approach for the serial measurement of patient-derived cancer organoid viability, thus opening new avenues for the application of these models to studies of cancer biology and therapy.
Using coexpression to explore cell-type diversity with the fcoex package
Authors: Lubiana Tiago , Nakaya Helder
Published: December 2021

Here, we present the fcoex package, which infers coexpression from scRNA-seq data and yields multiple, overlapping classes of cells based on coexpression modules. The tool extends the current scRNA-seq toolbox, providing a multi-hierarchy view on cell functionality and enabling the development of more complete cell atlases. Single-cell RNA sequencing (scRNA-seq) captures details of the cellular landscape, basing a fine-grained view on biological processes. Current pipelines, however, are restricted to single-label perspectives, missing details of the classification landscape. In the pbmc3k blood cell dataset, fcoex detects known classes, like antigen-presenting cells and a new theoretical group of cells, marked by the expression of FCGR3A (CD16). Fcoex extends the current scRNA-seq toolbox, providing a multi-hierarchy view on cell functions as a tool to develop complete cell type atlases.

Availability and Implementation

Fcoex is written in R and openly available in Bioconductor (https://bioconductor.org/packages/fcoex/).

Supplementary information

Supplementary data is available at the end of the manuscript. Source code for analysis is available at https://github.com/csbl-inovausp/fcoex_analysis;
The Spatial Reach of Neuronal Coherence and Spike-field Coupling across the Human Neocortex
Authors: Myers John C. , Smith Elliot H. , Leszczynski Marcin , O’Sullivan James , Yates Mark , McKhann Guy , Mesgarani Nima , Schroeder Charles , Schevon Catherine , Sheth Sameer A.
Published: December 2021

Neuronal coherence is thought to be a fundamental mechanism of communication in the brain, where synchronized field potentials coordinate synaptic and spiking events to support plasticity and learning. Although the spread of field potentials has garnered great interest, little is known about the spatial reach of phase synchronization, or neuronal coherence. Functional connectivity between different brain regions is known to occur across long distances, but the locality of coherence within a brain region is understudied. Here we used simultaneous recordings from electrocorticography (ECoG) grids and high-density microelectrode arrays to estimate the spatial reach of neuronal coherence and spike-field coherence (SFC) across frontal, temporal, and occipital cortices during cognitive tasks in humans. We observed the strongest coherence within a 2-3 cm distance from the microelectrode arrays, potentially defining an effective range for local communication. This range was relatively consistent across brain regions, spectral frequencies, and cognitive tasks. The magnitude of coherence showed power law decay with increasing distance from the microelectrode arrays, where the highest coherence occurred between ECoG contacts, followed by coherence between ECoG and deep cortical LFP, and then SFC (i.e., ECoG > LFP > SFC). The spectral frequency of coherence also affected its magnitude. Alpha coherence (8-14 Hz) was generally higher than other frequencies for signals nearest the microelectrode arrays, whereas delta coherence (1-3 Hz) was higher for signals that were farther away. Action potentials in all brain regions were most coherent with the phase of alpha oscillations, which suggests that alpha waves could play a larger, more spatially local role in spike timing than other frequencies. These findings provide a deeper understanding of the spatial and spectral dynamics of neuronal coherence, further advancing knowledge about how activity propagates across the human brain.
Reconfigurations in brain networks upon awakening from slow wave sleep: Interventions and implications in neural communication
Authors: Hilditch Cassie J. , Bansal Kanika , Chachad Ravi , Wong Lily R. , Bathurst Nicholas G. , Feick Nathan H. , Santamaria Amanda , Shattuck Nita L. , Garcia Javier O. , Flynn-Evans Erin E.
Published: December 2021

Sleep inertia is the brief period of impaired alertness and performance experienced immediately after waking. While the neurobehavioral symptoms of sleep inertia are well-described, less is known about the neural mechanisms underlying this phenomenon. A better understanding of the neural processes during sleep inertia may offer insight into the cognitive impairments observed and the awakening process generally. We observed brain activity following abrupt awakening from slow wave sleep during the biological night. Using electroencephalography (EEG) and a network science approach, we evaluated power, clustering coefficient, and path length across frequency bands under both a control condition and a blue-enriched light intervention condition in a within-subject design. We found that under control conditions, the awakening brain is typified by an immediate reduction in global theta, alpha, and beta power. Simultaneously, we observed a decrease in the clustering coefficient and an increase in path length within the delta band. Exposure to blue-enriched light immediately after awakening ameliorated these changes, but only for clustering. Our results suggest that long-range network communication within the brain is crucial to the waking process and that the brain may prioritize these long-range connections during this transitional state. Our study highlights a novel neurophysiological signature of the awakening brain and provides a potential mechanistic explanation for the effect of light in improving performance after waking.

One sentence summary

Blue-enriched light partially accelerates the rapid prioritization of long-range communication within the human brain that characterizes sleep inertia
What’s past is past, mostly: Brassicaceae host plants mask the feedback from the previous year’s soil history on bacterial communities, except when the Brassicaceae hosts experience drought
Authors: Blakney Andrew J.C. , Bainard Luke D. , St-Arnaud Marc , Hijri Mohamed
Published: December 2021

Previous soil history and the current plant hosts are two plant-soil feedbacks that operate at different time-scales to influence the structure soil bacterial communities. In this study, we used a MiSeq metabarcoding strategy to describe the impact of five Brassicaceae host plant species, and three different soil histories, on the structure of their bacterial root and rhizosphere communities at full flower. We found that the Brassicaceae host plants were consistently significant in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed nearly the same bacterial communities, regardless of soil history. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how plant-soil feedbacks operate at different time-scales and are involved in how microbial communities are structured is a pre-requisite for employing microbiome technologies in improving agricultural systems.
solPredict: Antibody apparent solubility prediction from sequence by transfer learning
Authors: Feng Jiangyan , Jiang Min , Shih James , Chai Qing
Published: December 2021

There is growing interest in developing therapeutic mAbs for the route of subcutaneous administration for several reasons, including patient convenience and compliance. This requires identifying mAbs with superior solubility that are amenable for high-concentration formulation development. However, early selection of developable antibodies with optimal high-concentration attributes remains challenging. Since experimental screening is often material and labor intensive, there is significant interest in developing robust in silico tools capable of screening thousands of molecules based on sequence information alone. In this paper, we present a strategy applying protein language modeling, named solPredict, to predict the apparent solubility of mAbs in histidine (pH 6.0) buffer condition. solPredict inputs embeddings extracted from pretrained protein language model from single sequences into a shallow neutral network. A dataset of 220 diverse, in-house mAbs, with extrapolated protein solubility data obtained from PEG-induced precipitation method, were used for model training and hyperparameter tuning through five-fold cross validation. An independent test set of 40 mAbs were used for model evaluation. solPredict achieves high correlation with experimental data (Spearman correlation coefficient = 0.86, Pearson correlation coefficient = 0.84, R2 = 0.69, and RMSE = 4.40). The output from solPredict directly corresponds to experimental solubility measurements (PEG %) and enables quantitative interpretation of results. This approach eliminates the need of 3D structure modeling of mAbs, descriptor computation, and expert-crafted input features. The minimal computational expense of solPredict enables rapid, large-scale, and high-throughput screening of mAbs during early antibody discovery.
Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting
Authors: Sarkar Daipayan , Lee Hyungro , Vant John W. , Turilli Matteo , Vermaas Josh V. , Jha Shantenu , Singharoy Abhishek
Published: December 2021

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary-structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. We introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehy-drogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.
Standard Intein Gene Expression Ramps (SIGER) for protein-independent expression control
Authors: Fages-Lartaud Maxime , Mueller Yasmin , Elie Florence , Coutarde Gaston , Hohmann-Marriott Martin Frank
Published: December 2021

Coordination of multi-gene expression is one of the key challenges of metabolic engineering for the development of cell factories. Constraints on translation initiation and early ribosome kinetics of mRNA are imposed by features of the 5’UTR in combination with the start of the gene, referred to as the “gene ramp”, such as rare codons and mRNA secondary structures. These features strongly influence translation yield and protein quality by regulating ribosome distribution on mRNA strands. The utilization of genetic expression sequences, such as promoters and 5’UTRs in combination with different target genes leads to a wide variety of gene ramp compositions with irregular translation rates leading to unpredictable levels of protein yield and quality. Here, we present the Standard Intein Gene Expression Ramps (SIGER) system for controlling protein expression. The SIGER system makes use of inteins to decouple the translation initiation features from the gene of a target protein. We generated sequence-specific gene expression sequences for two inteins (DnaB and DnaX) that display defined levels of protein expression. Additionally, we used inteins that possess the ability to release the C-terminal fusion proteinin vivoto avoid impairment of protein functionality by the fused intein. Overall, our results show that SIGER systems are unique tools to mitigate the undesirable effects of gene ramp variation and to control the relative ratios of enzymes involved in molecular pathways. As a proof of concept of the potential of the system, we also used a SIGER system to express two difficult-to-produce proteins, GumM and CBM73.

Graphical abstract
Rapid bacterial and fungal successional dynamics in first year after Chaparral wildfire
Authors: Pulido-Chavez M. Fabiola , Randolph James W. J. , Zalman Cassandra , Larios Loralee , Homyak Peter M. , Glassman Sydney I.
Published: December 2021

The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition with Illumina MiSeq sequencing of 16S and ITS2 amplicons. Fire severely reduced bacterial biomass by 47%, bacterial richness by 46%, fungal biomass by 86%, and fungal richness by 68%. The burned bacterial and fungal communities experienced rapid succession, with 5-6 compositional turnover periods. Analogous to plants, turnover was driven by “fire-loving” pyrophilous microbes, many of which have been previously found in forests worldwide and changed markedly in abundance over time. Fungal secondary succession was initiated by the Basidiomycete yeastGeminibasidium, which traded off against the filamentous AscomycetesPyronema,Aspergillus, andPenicillium. For bacteria, the ProteobacteriaMassiliadominated all year, but the FirmicuteBacillusand ProteobacteriaNoviherbaspirillumincreased in abundance over time. Our high-resolution temporal sampling allowed us to capture post-fire microbial secondary successional dynamics and suggest that putative tradeoffs in thermotolerance, colonization, and competition among dominant pyrophilous microbes control microbial succession with possible implications for ecosystem function.
Structural basis for the peptidoglycan editing activity of YfiH
Authors: Lee Meng-Sheng , Hsieh Kan-Yen , Kuo Chiao-I , Lee Szu-Hui , Chang Chung-I
Published: December 2021

Bacterial cells are encased in peptidoglycan (PG), a polymer of disaccharide N-acetyl-glucosamine (GlcNAc) and N-acetyl-muramic acid (MurNAc) cross-linked by peptide stems. PG is synthesized in the cytoplasm as UDP-MurNAc-peptide precursors, of which the amino-acid composition of the peptide is unique, with L-Ala added at the first position in most bacteria but L-Ser or Gly in some bacteria. YfiH is a PG-editing factor whose absence causes misincorporation of L-Ser instead of L-Ala into peptide stems; but its mechanistic function is unknown. Here we report the crystal structures of substrate-bound and product-bound YfiH, showing that YfiH is a cytoplasmic amidase that controls the incorporation of the correct amino acid to the nucleotide precursors by preferentially cleaving the nucleotide precursor byproduct UDP-MurNAc-L-Ser. This work reveals an editing mechanism in the cytoplasmic steps of peptidoglycan biosynthesis.
Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation
Authors: Wang Jinfan , Alvarado Carlos , Shin Byung-Sik , Bohlen Jonathan , Dever Thomas E. , Puglisi Joseph D.
Published: December 2021

How the eukaryotic 43S preinitiation complex scans along the 5′ untranslated region (5′UTR) of a capped mRNA to locate the correct start codon remains elusive. Here, we directly track yeast 43S-mRNA binding, scanning, and 60S subunit joining by real-time single-molecule fluorescence spectroscopy. Once engaged with the mRNA, 43S scanning occurs at >100 nucleotides per second, independent of multiple cycles of ATP-hydrolysis by RNA helicases. The scanning ribosomes can proceed through RNA secondary structures, but 5′UTR hairpin sequences near start codons drive scanning ribosomes at start codons back in the 5′ direction, requiring rescanning to arrive once more at a start codon. Direct observation of scanning ribosomes provides a mechanistic framework for translational regulation by 5′UTR structures and upstream near-cognate start codons.

One Sentence Summary

Direct observation of scanning eukaryotic ribosomes establishes a quantitative framework of scanning and its regulation.
Heterogeneity of the GFP fitness landscape and data-driven protein design
Authors: Somermeyer Louisa Gonzalez , Fleiss Aubin , Mishin Alexander S. , Bozhanova Nina G. , Igolkina Anna A. , Meiler Jens , Pujol Maria-Elisenda Alaball , Putintseva Ekaterina V. , Sarkisyan Karen S. , Kondrashov Fyodor A.
Published: December 2021

Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Counterintuitively, mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.
The p97-UBXD8 complex modulates ER-Mitochondria contact sites by modulating membrane lipid saturation and composition
Authors: Ganji Rakesh , Paulo Joao A. , Xi Yuecheng , Kline Ian , Zhu Jiang , Clemen Christoph S. , Weihl Conrad C. , Purdy John G. , Gygi Steve P. , Raman Malavika
Published: December 2021

The intimate association between the endoplasmic reticulum (ER) and mitochondrial membranes at ER-mitochondria contact sites serves as a platform for several critical cellular processes, in particular lipid synthesis. Enzymes involved in lipid biosynthesis are enriched at contacts and membrane lipid composition at contacts is distinct relative to surrounding membranes. How contacts are remodeled and the subsequent biological consequences of altered contacts such as perturbed lipid metabolism remains poorly understood. Here we show that the p97 AAA-ATPase and its ER-tethered ubiquitin-X domain adaptor 8 (UBXD8) regulate the prevalence of ER-mitochondria contacts. The p97-UBXD8 complex localizes to contacts and loss of this complex increases contacts in a manner that is dependent on p97 catalytic activity. Quantitative proteomics of purified contacts demonstrates alterations in proteins regulating lipid metabolism upon loss of UBXD8. Furthermore, lipidomics studies indicate significant changes in distinct lipid species in UBXD8 knockout cells. We show that loss of p97-UBXD8 results in perturbed contacts due to an increase in membrane lipid saturation via SREBP1 and the lipid desaturase SCD1. Aberrant contacts in p97-UBXD8 loss of function cells can be rescued by supplementation with unsaturated fatty acids or overexpression of SCD1. Perturbation of contacts and inherent lipid synthesis is emerging as a hallmark to a variety of human disorders such as neurodegeneration. Notably, we find that the SREBP1-SCD1 pathway is negatively impacted in the brains of mice with p97 mutations that cause neurodegeneration. Our results suggest that contacts are exquisitely sensitive to alterations to membrane lipid composition and saturation in a manner that is dependent on p97-UBXD8.
A novel multi-functional role for the MCM8/9 helicase complex in maintaining fork integrity during replication stress
Authors: Griffin Wezley C. , McKinzey David R. , Klinzing Kathleen N. , Baratam Rithvik , Trakselis Michael A.
Published: December 2021

The minichromosome maintenance (MCM) 8/9 helicase is a AAA+ complex involved in DNA replication-associated repair. Despite high sequence homology to the MCM2-7 helicase, an active role for MCM8/9 has remained elusive. We interrogated fork progression in cells lacking MCM8 or 9 and find there is a functional partitioning. Loss of MCM8 or 9 slows overall replication speed and increases markers of genomic damage and fork instability, further compounded upon treatment with hydroxyurea. MCM8/9 acts upstream and antagonizes the recruitment of BRCA1 in nontreated conditions. However, upon treatment with fork stalling agents, MCM9 recruits Rad51 to protect and remodel persistently stalled forks. The helicase function of MCM8/9 aids in normal replication fork progression, but upon excessive stalling, MCM8/9 directs additional stabilizers to protect forks from degradation. This evidence defines novel multifunctional roles for MCM8/9 in promoting normal replication fork progression and promoting genome integrity following stress.
Structural basis for substrate recognition, ligation and activation by a hyperactive Asn peptide ligase from Viola yedoensis
Authors: Hu Side , Sahili Abbas El , Kishore Srujana , Wong Yee Hwa , Hemu Xinya , Goh Boon Chong , Wang Zhen , Tam James P. , Liu Chuan-Fa , Lescar Julien
Published: December 2021

Peptide asparaginyl ligases (PALs) belong to a limited class of enzymes from cyclotide-producing plants, that perform site-specific ligation reactions after a target peptide Asx (Asn/Asp) binds to the ligase active site. How PALs specifically recognize their polypeptide substrates has remained elusive especially at the prime binding side of the enzyme. Here we captured VyPAL2, a catalytically efficient PAL from Viola yedoensis, in an activated state, with and without a bound substrate. The bound structure shows one ligase with the N-terminal polypeptide tail from another ligase molecule trapped at its active site, revealing how Asx inserts in the enzyme’s S1 pocket and why a hydrophobic residue is required at the substrate P2’ position. Beside illustrating the role played by P1 and P2’ residues as primary anchors for the enzyme reaction, these results provide a mechanistic explanation for the role of the “Gatekeeper” residue at the surface of the S2 pocket, in shifting the non-prime portion of the substrate and, as a result, the activity towards either ligation or hydrolysis. These results detail the molecular events that occur during proenzyme maturation in the plant vacuolar compartment, suggest a mechanism for ligation, and will inform the design of peptide ligases with tailored specificities.

One sentence summary

We captured VyPAL2, a catalytically efficient plant peptide ligase with a bound substrate, providing the molecular basis for substrate recognition and ligation.
Mosaicism and the taxonomy of human disease
Authors: Biesecker Leslie G.
Published: December 2021

Two papers in this special issue of Cold Spring Harbor Molecular Case Studies on Mosaicism throw light on an interesting conundrum in mosaic disorders. This conundrum centers on thresholds for the definition of mosaic disorders and how to reconcile the incredible inter- and intrapatient variability of mosaic disorders with the clinical imperative to have clear and distinct categorical diagnoses.
Effects of employee identity salience on content sharing in social networks
Authors: Zhang Xueting , Tang Tanya (Ya) , Chen Man , Wang Feng
Published: December 2021

Purpose

This research explores whether, when and why employee identity salience influences content sharing of employee's friends in social networks and further investigates two moderating conditions of network overlap and deal content.

Design/methodology/approach

In Study 1, the authors analyzed a field data related to 20,715 users on the largest social network platform in China. In Studies 2 and 3, the authors verified the findings of Study 1 and tested the underlying mechanism with two experiments.

Findings

The results showed that employee identity salience could increase sharing likelihood of content receiver, especially when the employee had higher network overlap with receiver. However, when the content contained deal-related information, the receiver was less likely to share this content from employee with salient identity. The authors also found that perceived information credibility acted as a mediator in above relationships.

Originality/value

This research is the first to test the effects of employee identity salience on content sharing by considering both content type and network characteristics. The authors also provide insights into the mediating role of information credibility, which enriches the content sharing and social network literature.
Situated rationalities and management control change – an empirical note on key actors, situated rationalities and generalised practices
Authors: Bertz Julie , Quinn Martin
Published: December 2021

Purpose

This paper aims to offer an incremental contribution, augmenting the notion of situated rationality as proposed by terBogt and Scapens (2019). Through insights from empirical data, the authors explore the role of situated rationalities of key individual actors in processes of management control change.

Design/methodology/approach

A qualitative research approach was adopted with qualitative data collected in a single public service organisation through face-to-face interviews, organisation documentation and observations.

Findings

The findings present the important role of key individual actors in bringing about a new situated rationality in a housing department. External austerity forces combined with actors’ experience rationalities acted as a stimulus to change existing management control practices in the management of public services.

Originality/value

The paper conceptualises “experience” rationality, capturing the experiences of a key actor, including elements of leadership style. Drawing on a story of a complex process of management control change, this paper thus reveals interactions between generalised practices and situated rationalities which were not highlighted by the extended framework of terBogt and Scapens.
School exclusion, substance misuse and use of weapons: an interpretative phenomenological analysis of interviews with children
Authors: Martin‐Denham Sarah
Published: December 2021

The study presents data drawn from semi‐structured interviews with five young people permanently excluded from schools in North East England. The research aimed to investigate the risk factors that lead to the children using illegal drugs, to determine the drivers and implications for drug misuse and the carrying of knives into school. The research also hoped to elicit from the young people, the solutions that could have prevented their exclusion from school. The interviews were analysed using interpretative phenomenological analysis to understand how a homogenous sample made sense of their lived experiences. The findings highlight the importance of prompt identification and support for children with learning and subsequent mental health needs as the evidence suggests they lead to perceived negative behaviours by teachers. The research provides further evidence that behaviour sanctions in mainstream schools such as detention and isolation booths do not improve behaviour but make it worse. Original to this research is the finding that children are consuming drugs before school to cope with their inability to access the learning, to aid their concentration and to medicate themselves to reduce the likelihood of being sanctioned by teachers.
The impact of digital transformation on female career development: dividends or divide? An empirical analysis based on the World Bank Survey Data on Chinese manufacturing companies
Authors: Chen Fei , Liu Zheng , Cui Weijun , Han Shuo , Jiang Nongjuan
Published: December 2021

Information and Communications Technology (ICT) has become an important force to promote the development of enterprises, but its impact on female career development is still controversial, mainly because existing studies have not gone deep into the operational level of enterprise ICT, have not focused on the research into the use environment of ICT, and have been lacking in quantitative analysis. In this article, empirical analysis is conducted through the use of the World Bank Survey Data on Chinese Manufacturing Companies 2012 and the Chinese General Social Survey, plus the adoption of the logit model. These studies reveal that 1) the degree of enterprise informatization and the degree of IT (information technology) support can significantly promote female career development, and 2) in terms of the influence mechanism, gender culture plays an intermediary role, i.e. ICT affects female career development by promoting an equal gender culture.
Identifying the influence of terrestrial–aquatic connectivity on palaeoecological inferences of past climate in Arctic lakes
Authors: Niemeyer Alannah M. , Medeiros Andrew S. , Todd Anthony , Wolfe Brent B.
Published: December 2021

Increased hydrological connectivity due to permafrost degradation is likely to have substantial implications for shallow aquatic systems common to sub‐arctic landscapes due to changes to overland and subsurface flow of water and transport of sediments and dissolved nutrients. Here, we explore the influence of increased connectivity on aquatic productivity based on multi‐parameter palaeolimnological analysis of two lakes located near Inuvik (Northwest Territories, Canada). We contrast a lake with little evidence of permafrost degradation in the surrounding area (Lake PG03) to one that has multiple connections to the terrestrial landscape through a network of thaw polygons in the lake catchment (Lake PG09). Comparisons of biological indicators (chironomids) and organic carbon and nitrogen elemental and isotope composition reveal recent divergent lake histories. The chironomid assemblage of Lake PG03 followed an expected temperature gradient, with a warming signal evident since ˜1970 CE, whereas the chironomid assemblage of Lake PG09 was found to primarily respond to nutrient availability and changes in habitat, likely as a result of increasing hydrological connectivity to the landscape. Rapid assemblage and habitat change along with a prominent increase in chironomid abundance were observed at Lake PG09 after ˜1960 CE, following a shift to greater inputs from the terrestrial environment as indicated by high C:N ratios (>15) and low δ13Corg (−30‰). Increased aquatic productivity following high allochthonous additions (˜1960–2014 CE) is supported by decreased C:N and rapidly increasing organic matter (Corg, N). These results demonstrate that increased connectivity along the terrestrial–aquatic interface for lakes is likely to foster elevated productivity in the future. Likewise, increased production poses a challenge to chironomid‐inferred July air temperature reconstructions in lakes that are less resilient to secondary gradients, where analogue mismatches can occur due to shifts in dominance of indicators that are orthogonal to the temperature gradient.
The independent and joint contribution of objective and subjective socioeconomic status on oral health indicators
Authors: Schuch Helena S. , Peres Karen G. , Haag Dandara G. , Boing Antonio F. , Peres Marco A.
Published: December 2021

Objectives

The understanding of how subjective socioeconomic status (SSS) relates to objective socioeconomic status (OSS), and how both conditions act together in oral health outcomes is still unclear. This study aims to test the independent and joint association between OSS and SSS with oral health, to assess the role of socioeconomic status discrepancies, and to evaluate the role of SSS in the association between OSS and oral health.

Methods

Data from 1140 adults from a population‐based study in Southern Brazil were used. We applied diagonal reference models DRM to disentangle the effects of OSS (education) and SSS (MacArthur Scale) to oral health outcomes. The outcomes were functional dentition clinically evaluated (FD ≥20 teeth) and self‐reported oral health SROH. We also examined the discrepancy between OSS and SSS to oral health indicators and the effect measure modification (EMM) of SSS on the association between OSS and oral health.

Results

Subjective socioeconomic status and OSS contributed equally to SROH, while OSS explained a substantially higher amount of FD than SSS (0.85 vs 0.15). An EMM of SSS was found on the association between OSS and fair/poor SROH, with a relative excess risk due to interaction (RERI) of 1.08. Less evidence of EMM was found for FD (RERI = 0.14). Individuals with lower SSS and OSS had four times the risk of the outcomes than the reference group.

Conclusions

Adults with concordant lower SSS and OSS have a worse oral health than those with concordant higher status. There was evidence that the association between OSS and SROH is modified by SSS.
The stability of social categories
Authors: Roth Abraham Sesshu
Published: December 2021

One important thesis Ásta defends in Categories We Live By is that social properties and categories are somehow dependent on our thoughts, attitudes, or practices—that they are inventions of the mind, projected onto the world. Another important aspect of her view is that the social properties are related to certain base properties; an individual is placed in a category when the relevant base properties are thought to hold of them. I see the relationship between the social and the base as connected to the problem of explaining how the social properties are sufficiently stable so as to be taken seriously, both in theoretical endeavors as well as in practical matters of how we relate to each other. In this light, I identify stability constraints for an adequate account of social categories. I argue that certain distinctive aspects of Ásta's conferralist view of social categories, such as the radical contextualism in her account of gender, undermine the stability of categories and are at odds with taking social categories seriously. I end with the suggestion that a distinctive “sheltered” form of normativity might help us do justice to Ásta's insights while avoiding some of the destabilizing elements of conferralism.
Number of growth days and not length of the growth period determines radial stem growth of temperate trees
Authors: Etzold Sophia , Sterck Frank , Bose Arun K. , Braun Sabine , Buchmann Nina , Eugster Werner , Gessler Arthur , Kahmen Ansgar , Peters Richard L. , Vitasse Yann , Walthert Lorenz , Ziemińska Kasia , Zweifel Roman
Published: December 2021

Radial stem growth dynamics at seasonal resolution are essential to understand how forests respond to climate change. We studied daily radial growth of 160 individuals of seven temperate tree species at 47 sites across Switzerland over 8 years. Growth of all species peaked in the early part of the growth season and commenced shortly before the summer solstice, but with species‐specific seasonal patterns. Day length set a window of opportunity for radial growth. Within this window, the probability of daily growth was constrained particularly by air and soil moisture, resulting in intermittent growth to occur only on 29 to 77 days (30% to 80%) within the growth period. The number of days with growth largely determined annual growth, whereas the growth period length contributed less. We call for accounting for these non‐linear intra‐annual and species‐specific growth dynamics in tree and forest models to reduce uncertainties in predictions under climate change.