bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal filters in response to presynaptic spike trains: Interplay of cellular, synaptic and short-term plasticity time scales
Authors: Mondal Yugarshi , Pena Rodrigo F. O. , Rotstein Horacio G.
Published: September 2021

Temporal filters, the ability of postsynaptic neurons to preferentially select certain presynaptic input patterns over others, have been shown to be associated with the notion of information filtering and coding of sensory inputs. Short-term plasticity (depression and facilitation; STP) has been proposed to be an important player in the generation of temporal filters. We carry out a systematic modeling, analysis and computational study to understand how characteristic postsynaptic (low-, high- and band-pass) temporal filters are generated in response to periodic presynaptic spike trains in the presence STP. We investi-gate how the dynamic properties of these filters depend on the interplay of a hierarchy of processes, including the arrival of the presynaptic spikes, the activation of STP, its effect on the excitatory synaptic connection efficacy, and the response of the postsynaptic cell. These mechanisms involve the inter-play of a collection of time scales that operate at the single-event level (roughly, during each presynaptic interspike-interval) and control the long-term development of the temporal filters over multiple presynaptic events. These time scales are generated at the levels of the presynaptic cell (captured by the presynaptic interspike-intervals), short-term depression and facilitation, synaptic dynamics and the post-synaptic cellular currents. We develop mathematical tools to link the single-event time scales with the time scales governing the long-term dynamics of the resulting temporal filters for a relatively simple model where depression and facilitation interact at the level of the synaptic efficacy change. We extend our results and tools to account for more complex models. These include multiple STP time scales and non-periodic presynaptic inputs. The results and ideas we develop have implications for the understanding of the generation of temporal filters in complex networks for which the simple feedforward network we investigate here is a building block.
Donor Macrophages Modulate Rejection after Heart Transplantation
Authors: Kopecky BJ , Dun H , Amrute JM , Lin CY , Bredemeyer AL , Terada Y , Bayguinov PO , Koenig AL , Frye CC , Fitzpatrick JAJ , Kreisel D , Lavine KJ
Published: September 2021

Background

Cellular rejection after heart transplantation imparts significant morbidity and mortality. Current immunosuppressive strategies are imperfect, target recipient T-cells, and have a multitude of adverse effects. The innate immune response plays an essential role in the recruitment and activation of T-cells. Targeting the donor innate immune response would represent the earliest interventional opportunity within the immune response cascade. There is limited knowledge regarding donor immune cell types and functions in the setting of cardiac transplantation and no current therapeutics exist for targeting these cell populations.

Methods

Using genetic lineage tracing, cell ablation, and conditional gene deletion, we examined donor mononuclear phagocyte diversity and function during acute cellular rejection of transplanted hearts in mice. We performed single cell RNA sequencing on donor and recipient macrophages, dendritic cells, and monocytes at multiple timepoints after transplantation. Based on our single cell RNA sequencing data, we evaluated the functional relevance of donor CCR2+and CCR2-macrophages using selective cell ablation strategies in donor grafts prior to transplant. Finally, we perform functional validation of our single cell-derived hypothesis that donor macrophages signal through MYD88 to facilitate cellular rejection.

Results

Donor macrophages persisted in the transplanted heart and co-existed with recipient monocyte-derived macrophages. Single-cell RNA sequencing identified donor CCR2+and CCR2-macrophage populations and revealed remarkable diversity amongst recipient monocytes, macrophages, and dendritic cells. Temporal analysis demonstrated that donor CCR2+and CCR2-macrophages were transcriptionally distinct, underwent significant morphologic changes, and displayed unique activation signatures after transplantation. While selective depletion of donor CCR2-macrophages reduced allograft survival, depletion of donor CCR2+macrophages prolonged allograft survival. Pathway analysis revealed that donor CCR2+macrophages were being activated through MYD88/NF-ĸβ signaling. Deletion of MYD88 in donor macrophages resulted in reduced antigen presenting cell recruitment, decreased emergence of allograft reactive T-cells, and extended allograft survival.

Conclusions

Distinct populations of donor and recipient macrophages co-exist within the transplanted heart. Donor CCR2+macrophages are key mediators of allograft rejection and inhibition of MYD88 signaling in donor macrophages is sufficient to suppress rejection and extend allograft survival. This highlights the therapeutic potential of donor heart-based interventions.
Serotype-based evaluation of an optogenetic construct in rat cortical astrocytes
Authors: Balachandar Lakshmini , Borrego Diana , Diaz Jorge Riera
Published: September 2021

Optogenetics is a modern technique which has been recently expanded to non-neuronal cell types, e.g., astrocytes, and involves targeted gene delivery of light-sensitive ion channels like Channelrhodopsin-2 (ChR2). Optogenetic regulation of astrocytic activity can be used for therapeutic intervention of several neurological disorders. Astrocytic gene delivery, viz adeno-associated viral (AAV) vectors, have proven to be robust, time-, and cost-efficient contrary to the generation of transgenic animal models. When transducing astrocytes with an AAV vector, it is imperative to perform a serotype evaluation of the AAV vector due to variability in serotype transduction efficiency depending on species, target region and construct length. Rats have been a very successful animal model for studying a variety of brain disorders, from which ChR2-based intervention of astrocytes will benefit. However, the most efficient AAV capsid serotype targeting astrocytes for ChR2 expression in the in vivo rat brain cortex has not been characterized. To address this, we have evaluated AAV serotypes 1, 5, and 8 of the vector AAV-GFAP-hChR2(H134)-mCherry targeting astrocytes in the rat brain neocortex. Results show that serotype 8 exhibits promising transduction patterns, as it has demonstrated the highest tangential and radial viral spread in the rat brain. Our research will facilitate translational research for future applications of optogenetics involving the transduction of rat brain cortical astrocytes.
Non-lesional and Lesional Lupus Skin Share Inflammatory Phenotypes that Drive Activation of CD16+ Dendritic Cells
Authors: Billi Allison C. , Ma Feiyang , Plazyo Olesya , Gharaee-Kermani Mehrnaz , Wasikowski Rachael , Hile Grace A. , Xing Xianying , Yee Christine M. , Rizvi Syed M. , Maz Mitra P. , Wen Fei , Tsoi Lam C. , Pellegrini Matteo , Modlin Robert L. , Gudjonsson Johann E. , Kahlenberg J. Michelle
Published: September 2021

Cutaneous lupus erythematosus (CLE) is a disfiguring and poorly understood condition frequently associated with systemic lupus. Studies to date suggest that non-lesional keratinocytes play a role in disease predisposition, but this has not been investigated in a comprehensive manner or in the context of other cell populations. To investigate CLE immunopathogenesis, normal-appearing skin, lesional skin, and circulating immune cells from lupus patients were analyzed via integrated single-cell RNA-sequencing and spatial-seq. We demonstrate that normal-appearing skin of lupus patients represents a type I interferon-rich, ‘prelesional’ environment that skews gene transcription in all major skin cell types and dramatically distorts cell-cell communication. Further, we show that lupus-enriched CD16+ dendritic cells undergo robust interferon education in the skin, thereby gaining pro-inflammatory phenotypes. Together, our data provide a comprehensive characterization of lesional and non-lesional skin in lupus and identify a role for skin education of CD16+ dendritic cells in CLE pathogenesis.
Activity-dependent modulation of NMDA receptors by endogenous zinc shapes dendritic function in cortical neurons
Authors: Morabito Annunziato , Zerlaut Yann , Serraz Benjamin , Sala Romain , Paoletti Pierre , Rebola Nelson
Published: September 2021

Activation of NMDA receptors (NMDARs) has been proposed to be a key component of single neuron computations in vivo. However is unknown if specific mechanisms control the function of such receptors and modulate input-output transformations performed by cortical neurons under in vivo-like conditions. Here we found that in layer 2/3 pyramidal neurons (L2/3 PNs), repeated synaptic stimulation results in an activity-dependent decrease in NMDARs activity by vesicular zinc. Such a mechanism shifted the threshold for dendritic non-linearities and strongly reduced LTP induction. Modulation of NMDARs was cell- and pathway-specific, being present selectively in L2/3-L2/3 connections but absent in ascending bottom-up inputs originating from L4 neurons. Numerical simulations highlighted that activity-dependent modulation of NMDARs has an important influence in dendritic computations endowing L2/3 PN dendrites with the ability to sustain dendritic non-linear integrations constant across different regimes of synaptic activity like those found in vivo. The present results therefore provide a new perspective on the action of vesicular zinc in cortical circuits by highlighting the role of this endogenous ion in normalizing dendritic integration of PNs during a constantly changing synaptic input pattern.
Taxonomy Analysis in Bacterial Kingdom based on Protein Domain: A Comparison Study
Authors: Wang Boqian , Zhou Jianglin , Jin Yuan , Hu Mingda , Zhao Yunxiang , Wang Xin , Yang Haoyi , Gong Xingfei , Zhang Fengwei , Zhang Zehan , Kang Fuqiang , Liang Long , Yue Junjie , Ren Hongguang
Published: September 2021

The taxonomy research on the bacterial kingdom is important and can be usually conducted by the analysis on conserved genes, 16s rRNA, protein domain, and so on. Comparatively, the protein domains maintain a most direct relationship with phenotypes. In this paper, based on the protein domain, we propose a 3-step framework to standardize the classification process of bacteria. Different model candidates are involved and discussed in each step. By comparing the classification results with existing taxonomy, we select the most appropriate candidate to improve the framework, and furthermore, discuss their biological significance. Finally, we put forward taxonomy suggestions based on the best classification results.

Significance Statement

We standardize a 3-step framework to carry out bacterial taxonomy research based on protein domain. Furthermore, we filter out the best solution in each step that can together generate the most appropriate classification result, and at the same time, we discuss the biological significant it indicates. Finally, we propose suggestions on NCBI bacterial taxonomy based on the classification results.
Single-cell profiling reveals periventricular CD56bright NK cell accumulation in multiple sclerosis
Authors: Rodríguez-Lorenzo Sabela , van Olst Lynn , Rodriguez-Mogeda Carla , Kamermans Alwin , van der Pol Susanne M.A. , Rodríguez Ernesto , Kooij Gijs , de Vries Helga E.
Published: September 2021

Multiple sclerosis (MS) is a chronic demyelinating disease characterised by immune cell infiltration resulting in lesions that preferentially affect periventricular areas of the brain. Despite research efforts to define the role of various immune cells in MS pathogenesis, the focus has been on a few immune cell populations while full-spectrum analysis, encompassing others such as natural killer (NK) cells, has not been performed. Here, we used single-cell mass cytometry (CyTOF) to profile the immune landscape of brain periventricular areas – septum and choroid plexus – and blood from MS donors and controls with and without other neurological diseases. Using a 37-marker panel, we revealed the infiltration of T cells and antibody-secreting cells in periventricular brain regions and identified a novel NK cell signature specific to MS. CD56bright NK cells accumulated in the septum of MS donors, displaying an activated and migratory phenotype that was similar to that of CD56bright NK cells in their circulation. We validated this signature by multiplex immunohistochemistry and found that NK cells with high expression of granzyme K, which is typical of the CD56bright subset, accumulated in both periventricular lesions and the choroid plexus. Together, our multi-tissue single-cell data suggests that CD56bright NK cells infiltrate the periventricular brain regions in MS patients via both the blood-brain and blood-CSF barriers and brings NK cells to the spotlight of MS pathology.
Determining jumping performance from a single body-worn accelerometer using machine learning
Authors: White Mark , Bezodis Neil , Neville Jonathon , Summers Huw , Rees Paul
Published: September 2021

External peak power in the countermovement jump is frequently used to monitor athlete training. The gold standard method uses force platforms, but they are unsuitable for field-based testing. However, alternatives based on jump flight time or Newtonian methods applied to inertial sensor data have not been sufficiently accurate for athlete monitoring. Instead, we developed a machine learning model based on characteristic features (functional principal components) extracted from a single body-worn accelerometer. Data were collected from 69 male and female athletes at recreational, club or national levels, who performed 696 jumps in total. We considered vertical countermovement jumps (with and without arm swing), sensor anatomical locations, machine learning models and whether to use resultant or triaxial signals. Using a novel surrogate model optimisation procedure, we obtained the lowest errors with a support vector machine when using the resultant signal from a lower back sensor in jumps without arm swing. This model had a peak power RMSE of 2.3 W·kg-1 (5.1% of the mean), estimated using nested cross validation and supported by an independent holdout test (2.0 W·kg-1). This error is lower than in previous studies, although it is not yet sufficiently accurate for a field-based method. Our results demonstrate that functional data representations work well in machine learning by reducing model complexity in applications where signals are aligned in time. Our optimisation procedure also was shown to be robust can be used in wider applications with low-cost, noisy objective functions.
The dissociable effects of reward on sequential motor behaviour
Authors: Sporn Sebastian , Chen Xiuli , Galea Joseph M
Published: September 2021

Reward has consistently been shown to enhance motor performance however its beneficial effects appear to be largely unspecific. While reward has been shown to invigorate performance, it also enhances learning and/or retention. Therefore, a mechanistic account of the effects of reward on motor behaviour is lacking. Here we tested the hypothesis that these distinct reward-based improvements are driven by dissociable reward types: explicit reward (i.e. money) and performance feedback (i.e. points). Experiment 1 showed that explicit reward instantaneously improved movement times (MT) using a novel sequential reaching task. In contrast, performance-based feedback led to learning-related improvements. Importantly, pairing both maximised MT performance gains and accelerated movement fusion. Fusion describes an optimisation process during which neighbouring sequential movements blend together to form singular actions. Results from experiment 2 served as a replication and showed that fusion led to enhanced performance speed whilst also improving movement efficiency through increased smoothness. Finally, experiment 3 showed that these improvements in performance persist for 24 hours even without reward availability. This highlights the dissociable impact of explicit reward and performance feedback, with their combination maximising performance gains and leading to stable improvements in the speed and efficiency of sequential actions.
Extensive Chromatin Structure-Function Association Revealed by Accurate Compartmentalization Characterization
Authors: Wen Zi , Zhang Weihan , Zhong Quan , Xu Jinsheng , Hou Chunhui , Qin Zhaohui , Li Li
Published: September 2021

Chromosome conformation capture-based experiments have shown that eukaryotic chromosomes are partitioned into A and B compartments conventionally identified by the first eigenvector (EV1) of dimension reduction methods. However, many genomic regions show marginal EV1 values, indicating the ambiguity of A/B compartment scheme on these regions. We develop MOSAIC (MOdularity and Singular vAlue decomposition-based Identification of Compartments), an accurate compartmental state detection scheme. MOSAIC reveals that those ambiguous regions segregate into two additional compartmental states, which typically correspond to small genomic regions flanked by large canonical A/B compartments with opposite activities. They are denoted as micro-compartments accordingly. In contrast to the canonical A/B compartments, micro-compartments cover ~30% of the genome and are highly dynamic between cell types. More importantly, distinguishing the micro-compartments underpins accurate characterization of chromatin structure-function relationship. By applying MOSAIC to GM12878 and K562 cells, we identify CD86, ILDR1 and GATA2 which show concordance between gene expression and compartmental states beyond the scheme of A/B compartments. Taken together, MOSAIC uncovers fine-scale and dynamic structures underlying canonical A/B compartments. Our results suggest dynamic chromatin compartmentalization is underlying transcriptional regulation and disease.
Group size planning of breedings of gene-modified animals
Authors: Milchevskaya Vladislava , Bugnon Philippe , ten Buren Emiel B.J. , Brand Frank , Tresch Achim , Buch Thorsten
Published: September 2021

Animal breeding is time-consuming, costly, and affected by stochastic events related to Mendelian genetics, fertility, and litter size. Careful planning is mandatory to ensure a successful outcome using the least number of animals, hence adhering to the 3Rs of animal welfare. We have developed an R package, accessible also through an interactive website, that optimizes breeding design and provides a comprehensive report suitable for any breeder of genetically defined traits.
AF-vapeR: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors
Authors: Whiting James R. , Paris Josephine R. , van der Zee Mijke J. , Fraser Bonnie A.
Published: September 2021

The repeatability of evolution at the genetic level has been demonstrated to vary along a continuum from complete parallelism to divergence. In order to better understand why this continuum exists within and among systems, hypotheses must be tested using high confidence sets of candidate loci for repeatability. Despite this, few methods have been developed to scan SNP data for signatures specifically associated with repeatability, as opposed to local adaptation.

Here we present AF-vapeR (Allele Frequency Vector Analysis of Parallel Evolutionary Responses), an approach designed to identify genome regions exhibiting highly correlated allele frequency changes within haplotypes and among replicated allele frequency change vectors. The method divides the genome into windows of an equivalent number of SNPs, and within each window performs eigen decomposition over normalised allele frequency change vectors (AFV), each derived from a replicated pair of populations/species. Properties of the resulting eigenvalue distribution can be used to compare regions of the genome for those exhibiting strong parallelism, and can also be compared against a null distribution derived from randomly permuted AFV. Further, the shape of the eigenvalue distribution can reveal multiple axes of parallelism within datasets.

We demonstrate the utility of this approach to detect different modes of parallel evolution using simulations, and also demonstrate a reduction in error rate compared with intersecting FST outliers. Lastly, we apply AF-vapeR to three previously published datasets (stickleback, guppies, and Galapagos finches) which comprise a range of sampling and sequencing strategies, and lineage ages. We detect known parallel regions whilst also identifying novel candidates.

The main benefits of this approach include a reduced false-negative rate under many conditions, an emphasis on signals associated specifically with repeatable evolution as opposed to local adaptation, and an opportunity to identify different modes of parallel evolution at the first instance.
Multi-objective prioritisation of candidate epitopes for diagnostic test development
Authors: Cerny Roman , Ashford Jodie , Reis-Cunha João , Campelo Felipe
Published: September 2021

Background

The development of peptide-based diagnostic tests requires the identification of epitopes that are at the same time highly immunogenic and, ideally, unique to the pathogen of interest, to minimise the chances of cross-reactivity. Existing computational pipelines for the prediction of linear B-cell epitopes tend to focus exclusively on the first objective, leaving considerations of cross-reactivity to later stages of test development.

Results

We present a multi-objective approach to the prioritisation of candidate epitopes for experimental validation, in the context of diagnostic test development. The dual objectives of uniqueness (measured as dissimilarity from known epitope sequences from other pathogens) and predicted immunogenicity (measured as the probability score returned by the prediction model) are considered simultaneously. Validation was performed using data from three distinct pathogens (namely the nematode Onchocerca volvulus, the Epstein-Barr Virus and the Hepatitis C Virus), with predictions derived using an organism-specific prediction approach. The multi-objective rankings returned sets of non-dominated solutions as potential targets for the development of diagnostic tests with lower probability of false positives due to cross-reactivity.

Conclusions

The application of the proposed approach to three test pathogens led to the identification of 20 new potential epitopes, with both high probability and a high degree of exclusivity to the target organisms. The results indicate the potential of the proposed approach to provide enhanced filtering and ranking of potential candidates, highlighting potential cross-reactivities and including this information into the test development process right from the target identification and prioritisation step.
Evaluation of cell segmentation methods without reference segmentations
Authors: Chen Haoran , Murphy Robert F.
Published: September 2021

Cell segmentation is a cornerstone of many bioimage informatics studies and inaccurate segmentation introduces error in downstream analysis. Evaluating segmentation results is thus a necessary step for developing segmentation methods as well as for choosing the most appropriate method for a particular type of sample. The evaluation process has typically involved comparison of segmentations to those generated by humans, which can be expensive and subject to unknown bias. We present here an approach to evaluating cell segmentation methods without relying upon comparison to results from humans. For this, we defined a number of segmentation quality metrics that can be applied to multichannel fluorescence images. We calculated these metrics for 14 previously-described segmentation methods applied to datasets from 4 multiplexed microscope modalities covering 5 tissues. Using principal component analysis to combine the metrics we defined an overall cell segmentation quality score and ranked the segmentation methods. We found that two deep learning-based methods performed the best overall, but that results for all methods could be significantly improved by postprocessing to ensure proper matching of cell and nuclear masks. Our evaluation tool is available as open source and all code and data are available in a Reproducible Research Archive.
Identification and Functional Annotation of Long Intergenic Non-coding RNAs in the Brassicaceae
Authors: Palos Kyle , Dittrich Anna C. Nelson , Yu Li’ang , Brock Jordan R. , Wu Larry , Sokolowska Ewelina , Skirycz Aleksandra , Hsu Polly , Lyons Eric , Beilstein Mark A. , Nelson Andrew D. L.
Published: September 2021

Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts with critical biological functions. Despite the wealth of RNA-seq data available, lincRNA identification lags in the plant lineage. In addition, there is a need for a harmonized identification and annotation effort to enable cross-species functional and genomic comparisons. In this study we processed >24 Tbp of RNA-seq data from >16,000 experiments to identify ~130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used Nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify functional motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our dataset with sequence or transcriptional evolutionary conservation, including lincRNAs transcribed adjacent to orthologous genes that display little sequence similarity and likely function as transcriptional regulators. Finally, we used guilt-by-association techniques to further classify these lincRNAs according to putative function. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, short ORFs, and whose expression is modulated by abiotic stress are a few of the annotations that will prioritize and guide future functional analyses.
Integrative Analysis of Spatial Transcriptome with Single-cell Transcriptome and Single-cell Epigenome in Mouse Lungs after Immunization
Authors: Xu Zhongli , Wang Xinjun , Fan Li , Wang Fujing , Wang Jiebiao , Chen Wei , Chen Kong
Published: September 2021

Immunological memory is key to productive adaptive immunity. An unbiased, high throughput gene expression profiling of tissue-resident memory T cells at their precise anatomical locations within the lung is fundamental to understanding lung immunity, but such spatial information has yet to be characterized. In this study, using a well-established Klebsiella pneumoniae infection model, we performed an integrative analysis of spatial transcriptome with single-cell RNA-seq and single-cell ATAC-seq on lung cells from mice after immunization using the 10x Genomics Chromium and Visium platform. We employed several deconvolution algorithms and established an optimized deconvolution pipeline to accurately decipher specific cell-type composition by anatomic location. We identified and located 12 major cell types by scRNA-seq and spatial transcriptomic analysis. Integrating scATAC-seq data from the same cells processed in parallel with scRNA-seq, we found epigenomic profiles provide more robust cell type identification, especially for lineage-specific T helper cells. When combining all three data modalities, we observed a dynamic change in the location of T helper cells as well as their corresponding chemokines for chemotaxis. Furthermore, cell-cell communication analysis of spatial transcriptome provided evidence of lineage-specific T helper cells receiving designated cytokine signaling. In summary, our first-in-class study demonstrated the power of multi-omics analysis to uncover intrinsic spatial- and cell-type-dependent molecular mechanisms of lung immunity. Our data provides a rich research resource of single cell multi-omics data as a reference for understanding spatial dynamics of lung immunization.
A ppGpp-mediated brake on photosynthesis is required for acclimation to nitrogen limitation in Arabidopsis
Authors: Romand Shanna , Abdelkefi Hela , Lecampion Cecile , Belaroussi Mohamed , Dussenne Melanie , Ksas Brigitte , Citerne Sylvie , Caius José , D’Alessandro Stefano , Fakhfakh Hatem , Caffarri Stefano , Havaux Michel , Field Ben
Published: September 2021

Guanosine pentaphosphate and tetraphosphate (together referred to as ppGpp) are hyperphosphorylated nucleotides found in bacteria and the chloroplasts of plants and algae. In plants and algae artificial ppGpp accumulation can inhibit chloroplast gene expression, and influence photosynthesis, nutrient remobilisation, growth, and immunity. However, it is so far unknown whether ppGpp is required for abiotic stress acclimation in plants. Here, we demonstrate that ppGpp biosynthesis is necessary for acclimation to nitrogen starvation in Arabidopsis. We show that ppGpp is required for remodeling the photosynthetic electron transport chain to downregulate photosynthetic activity and for protection against oxidative stress. Furthermore, we demonstrate that ppGpp is required for coupling chloroplastic and nuclear gene expression during nitrogen starvation. Altogether, our work indicates that ppGpp is a pivotal regulator of chloroplast activity for stress acclimation in plants.
Shedding light on biosilica morphogenesis by comparative analysis of the silica-associated proteomes from three diatom species
Authors: Skeffington Alastair W. , Gentzel Marc , Ohara Andre , Milentyev Alexander , Heintze Christoph , Böttcher Lorenz , Görlich Stefan , Shevchenko Andrej , Poulsen Nicole , Kröger Nils
Published: September 2021

Morphogenesis of the intricate patterns of diatom silica cell walls is a protein-guided process, yet to date only very few such silica morphogenetic proteins have been identified. Therefore, it is unknown whether all diatoms share conserved proteins of a basal silica forming machinery, and whether unique proteins are responsible for the morphogenesis of species specific silica patterns.

To answer these questions, we extracted proteins from the silica of three diatom species (Thalassiosira pseudonana, Thalassiosira oceanica and Cyclotella cryptica) by complete demineralization of the cell walls. LC-MS/MS analysis of the extracts identified 92 proteins that we name ‘Soluble Silicome Proteins’ (SSPs).

Surprisingly, no SSPs are common to all three species, and most SSPs showed very low similarity to one another in sequence alignments. In depth bioinformatics analyses revealed that SSPs can be grouped into distinct classes bases on short unconventional sequence motifs whose functions are yet unknown. The results from in vivo localization of selected SSPs indicates that proteins, which lack sequence homology but share unconventional sequence motifs may exert similar functions in the morphogenesis of the diatom silica cell wall.
Chromomycin A5 induces bonafide immunogenic cell death in metastatic melanoma
Authors: Florêncio Katharine G. D. , Edson Evelline A. , Pinto Francisco C. L. , Pessoa Otília D. L. , Machado-Neto João Agostinho , Wilke Diego V.
Published: September 2021

Some first-line cytotoxic chemotherapics, e.g. doxorubicin, paclitaxel and oxaliplatin, induce activation of the immune system through immunogenic cell death (ICD). Tumor cells undergoing ICD function as a vaccine, releasing damage-associated molecular patterns (DAMPs), which act as adjuvants, and neoantigens of the tumor are recognized as antigens. ICD induction is rare, however it yields better and long-lasting antitumor responses to chemotherapy. Advanced metastatic melanoma (AMM) is incurable for more than half of patients. The discovery of ICD inducers against AMM is an interesting drug discovery strategy with high translational potential. Here we evaluated ICD induction of four highly cytotoxic chromomycins A (CA5-8). B16-F10, a metastatic melanoma cell line, treated with CA5-8 and doxorubicin exhibited ICD features such as autophagy and apoptosis, externalization of calreticulin, and releasing of HMGB1. However, CA5-treated cells had the best profile, also inducing ATP release, ERp57 externalization, phosphorylation of eIF2α and altering expression of transcription of genes related to autophagy, endoplasmic reticulum stress, and apoptosis. Bonafide ICD induction by CA5 was confirmed by a C57BL/6 mice vaccination assay with CA5-treated cells. These findings support a high potential of CA5 as an anticancer candidate against AMM.
Willingness to wait covaries with endogenous variation in cortisol
Authors: Lukinova Evgeniya , Erlich Jeffrey C.
Published: September 2021

Stress is a normal part of our everyday lives. It alerts us to changes in our environment working as an early warning system. However, when stress is prolonged, it can become harmful. The deleterious effects of stress on brain function are well established: chronic stress significantly impairs cognitive function reducing our ability to solve problems and to regulate behavior and, therefore, may lead to more challenges that can further exacerbate stress. An important class of decisions that may be made under stress includes those between rewards delivered immediately vs. those delivered in the future. Not considering or devaluing future outcomes (delay discounting) can result in adverse outcomes such as not buying health insurance, gambling or drug use. To date, however, little is known about how chronic stress influences economic decisions that differ in the time of outcome delivery. A handful of studies suggest that increased stress may lead to more impulsive choices in subjects of average socioeconomic status and stress levels. Here, we addressed this gap by using a longitudinal design to determine whether chronic stress measures (via questionnaires, saliva and hair samples) are associated with the economic choices under different time scales within subject (N = 34). We found that the degree to which people think it is worth waiting, i.e. individual’s discount factor, over seconds, but not over days, varied reliably with endogenous stress. These results are imperative to studying stress in a variety of contexts: e.g., the variation in consumer’s impulse purchases could be attributed to the variation in individual stress responses to the environment, even in healthy adults.
Spatio-temporal analysis of remote sensing images provides early warning signals of forest mortality
Authors: Alibakhshi Sara
Published: September 2021

Ecosystems are under unprecedented pressures, reflected in rapid changes in the regime of disturbances that may cause negative impacts on them. This highlights the importance of characterizing the state of an ecosystem and its response to disturbances, which is known as a notoriously difficult task. The state-of-the-art knowledge has been tested rarely in real ecosystems for a number of reasons such as mismatches between the time scale of ecosystem processes and data accessibility as well as weaknesses in the performance of available methods. This study aims to use remotely sensed spatio-temporal data to identify early warning signals of forest mortality using satellite images. For this purpose, I propose a new approach that measures local spatial autocorrelation (using local Moran’s I and local Geary’s c method) at each time, which proved to produce robust results in multiple different study sites examined in this article. This new approach successfully generates early warning signals from time series of local spatial autocorrelation values in unhealthy study sites 2 years prior to forest mortality occurrence. Furthermore, I develop a new R package, called “stew”, that enables users to explore spatio-temporal analysis of ecosystem state changes. This work corroborates the suggestion that spatio-temporal indicators have the potential to diagnose early warning signals to identify upcoming climate-induced forest mortality, up to two years before its occurrence.
Dynamics of p53 DNA binding sites contributes to functional selectivity of p53-driven gene expression
Authors: Safieh Jessy , Chazan Ariel , Vyas Pratik , Saleem Hanna , Danin-Poleg Yael , Ron Dina , Haran Tali E.
Published: September 2021

The tumor suppressor protein p53 is situated in the midst of a complex network that is activated in response to cellular stress. An unresolved question is how p53 activates its myriad target genes in response to the severity of the stress signal and consequently coordinates the functional outcome in a timely manner. We have previously shown that DNA torsional flexibility distinguishes among p53 response elements (REs). Here we calculated the flexibility of over 200 p53 REs. By connecting functional pathways of p53-dependent genes to the calculated flexibility of their REs, we show that genes belonging to pathways activated rapidly upon stress (e.g., cell-cycle arrest, energy metabolism and innate immunity) contain REs that are significantly more flexible relative to REs of genes involved in pathways that need to be more strictly regulated or are activated later in the response to stress (e.g., intrinsic apoptosis and p53 negative regulation). The global structural properties of several p53 REs belonging to the different pathways were experimentally validated. Additionally, reporter gene expression driven by flexible p53 REs occurred at lower p53 levels and with faster rates than expression from rigid REs. Moreover, analysis of published endogenous mRNA levels of p53 target genes as a function of the flexibility of their REs support our hypothesis. Overall, we demonstrate that DNA flexibility of p53 REs contributes significantly to the timely expression of p53 target genes and thereby plays an important role in cell-faith decisions in the p53 circuity.
Novel biochemical, structural and systems insights into inflammatory signaling revealed by contextual interaction proteomics
Authors: Ciuffa Rodolfo , Uliana Federico , Mehnert Martin , Marulli Cathy , Satanowski Ari , Rodilla Ramírez Pilar Natalia , Meier Pascal , Ori Alessandro , Gstaiger Matthias , Aebersold Ruedi
Published: September 2021

Protein-protein interactions (PPI) represent the main mode of the proteome organization in the cell. In the last decade, several large-scale representations of PPI networks have captured generic aspects of the functional organization of network components, but mostly lack the context of cellular states. However, the generation of contextual representations of PPI networks is essential for structural and systems-level modeling of biological processes and remains an unsolved challenge. In this study we describe an integrated experimental/computational strategy to achieve a contextualized modeling of PPI. This strategy defines the composition, stoichiometry, spatio-temporal organization and cellular requirements for the formation of target assemblies. We used this approach to generate an integrated model of the formation principles and architecture of a large signalosome, the TNF-receptor signaling complex (TNF-RSC). Overall, we show that the integration of systems- and structure-level information provides a generic, largely unexplored link between the modular proteome and cellular function.

Significance Statement

In this work, we propose a critical shift in the way we analyze, and think the study of, protein-protein interactions (PPI), and present an experimental and computational framework to model them in the cellular context. We applied this framework to the signalosome tumor necrosis factor receptor signaling complex (TNF-RSC), and generated an integrated model of its formation and architecture that provides new insights and resolved controversies regarding its organization and regulation. To achieve a contextual modelling of PPIs, we first optimized and developed, and then combined, approaches to map the composition of a target complex, its absolute stoichiometry, its spatial organization and assembly/disassembly dynamics, its temporal dependence on signaling, and its reliance on cellular resources.
Ribosomal RNA 2’-O-methylations regulate translation by impacting ribosome dynamics
Authors: Khoshnevis Sohail , Dreggors-Walker R. Elizabeth , Marchand Virginie , Motorin Yuri , Ghalei Homa
Published: September 2021

Protein synthesis by ribosomes is critically important for gene expression in all cells. The ribosomal RNAs (rRNAs) are marked by numerous chemical modifications. An abundant group of rRNA modifications, present in all domains of life, is 2’-O-methylation guided by box C/D small nucleolar RNAs (snoRNAs) which are part of small ribonucleoprotein complexes (snoRNPs). Although 2’-O-methylations are required for proper production of ribosomes, the mechanisms by which these modifications contribute to translation have remained elusive. Here, we show that a change in box C/D snoRNP biogenesis in actively growing yeast cells results in the production of hypo 2’-O-methylated ribosomes with distinct translational properties. Using RiboMeth-Seq for the quantitative analysis of 2’-O methylations, we identify site-specific perturbations of the rRNA 2’-O-methylation pattern and uncover sites that are not required for ribosome production under normal conditions. Characterization of the hypo 2’-O-methylated ribosomes reveals significant translational fidelity defects including frameshifting and near-cognate start codon selection. Using rRNA structural probing, we show that hypo 2’-O-methylation affects the inherent dynamics of the ribosomal subunits and impacts the binding of translation factor eIF1 thereby causing translational defects. Our data reveal an unforeseen spectrum of 2’-O-methylation heterogeneity in yeast rRNA and suggest a significant role for rRNA 2’-O-methylation in regulating cellular translation by controlling ribosome dynamics and ligand binding.
Progenitor cell integration into a barrier epithelium during adult organ turnover
Authors: Moreno-Roman Paola , Su Yu-Han , Galenza Anthony , Acosta-Alvarez Lehi , Debec Alain , Guichet Antoine , Knapp Jon-Michael , Kizilyaprak Caroline , Humbel Bruno M. , Kolotuev Irina , O’Brien Lucy Erin
Published: September 2021

Barrier epithelial organs face the constant challenge of sealing the interior body from the external environment while simultaneously replacing the cells that contact this environment. These replacement cells—the progeny of basal stem cells—are born without apical, barrier-forming structures such as a protective, lumen-facing membrane and occluding junctions. How stem cell progeny acquire these structures to become part of the barrier is unknown. Here we use Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM), Correlative Light-Electron Microscopy (CLEM), and volumetric imaging of live and fixed organs to investigate progenitor integration in the intestinal epithelium of adult Drosophila. We find that stem cell daughters gestate their future lumenal-apical membrane beneath a transient, basal niche formed by an umbrella-shaped occluding junction that shelters the growing cell and adheres it to mature neighbor cells. The umbrella junction both targets formation of a deep, microvilli-lined, apical invagination and closes it off from the contents of the gut lumen. When the growing cell is sufficiently mature, the umbrella junction retracts to expose this Pre-Assembled Apical Compartment (PAAC) to the gut lumen, thus incorporating the new cell into the intestinal barrier. When we block umbrella junctions, stem cell daughters grow and attempt to differentiate but fail to integrate; when we block cell growth, no umbrella junctions form and daughters arrest in early differentiation. Thus, stem cell progeny build new barrier structures in the shelter of a transient niche, where they are protected from lumenal insults until they are prepared to withstand them. By coordinating this dynamic junctional niche with progenitor cell differentiation, a physiologically active epithelial organ incorporates new cells while upholding integrity of its barrier.
The master energy homeostasis regulator PGC-1α couples transcriptional co-activation and mRNA nuclear export
Authors: Mihaylov Simeon R. , Castelli Lydia M. , Lin Ya-Hui , Gül Aytac , Soni Nikita , Hastings Christopher , Flynn Helen R. , Dickman Mark J. , Snijders Ambrosius P. , Bandmann Oliver , Mortiboys Heather , Ultanir Sila K. , Hautbergue Guillaume M.
Published: September 2021

PGC-1α plays a central role in maintaining the mitochondrial and energy metabolism homeostasis, linking external stimuli to the transcriptional co-activation of genes involved in adaptive and age-related pathways. The carboxyl-terminus encodes a serine/arginine-rich (RS) region and a putative RNA recognition motif, however potential RNA-processing role(s) have remained elusive for the past 20 years. Here, we show that the RS domain of human PGC-1α directly interacts with RNA and the nuclear RNA export factor NXF1. Inducible depletion of endogenous PGC-1α and expression of RNAi-resistant RS-deleted PGC-1α further demonstrate that the RNA-binding activity is required for nuclear export of co-activated transcripts and mitochondrial homeostasis. Moreover, a quantitative proteomics approach confirmed PGC-1α-dependent RNA transport and mitochondrial-related functions, identifying also novel mRNA nuclear export targets in age-related telomere maintenance. Discovering a novel function for a major cellular homeostasis regulator provides new directions to further elucidate the roles of PGC-1α in gene expression, metabolic disorders, ageing and neurodegenerative diseases.
Mitochondrial UPR negatively regulates wounding-induced innate immune response in C. elegans epidermis
Authors: Zhao Jianzhi , Fu Hongying , Zhou Hengda , Ren Xuecong , Wang Yuanyuan , Xu Suhong
Published: September 2021

Tissue damage elicits a rapid innate immune response that is essential for efficient wound healing and survival of metazoans. It is well known that p38 MAPK kinase, TGF-β, and hemidesmosome signaling pathways have been involved in wounding-induced innate immunity in C. elegans. Here, we find that loss of function of ATFS-1 increased innate immune response while an elevated level of mitochondrial unfolded protein response (mitoUPR) inhibits the innate immune response upon epidermal wounding. Epidermal wounding triggers the nucleus export of ATFS-1 and inhibits themitoUPR in C. elegans epidermis. Moreover, genetic analysis suggests that ATFS-1 functions upstream of the p38 MAP kinase, TGF-β and DAF-16 signaling pathways in regulating AMPs induction. Thus, our results suggest that the mitoUPR function as an intracellular signal required to fine-tune innate immune response after tissue damage.

Highlights

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ATFS-1 inhibits the wounding-induced innate immune response in C. elegans

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mitoUPR inhibits wounding-induced innate immune response

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Epidermal wounding induces downregulation of ATFS-1 in the epidermis

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mitoUPR acts upstream of p38MAPK and TGF-β pathways to regulate innate immunity