bluuebunny/crossref_metadata_2025 huggingface dataset:
The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes
Authors: Garipler Görkem , Lu Congyi , Morrissey Alexis , Lopez-Zepeda Lorena S. , Vidal Simon E. , Aydin Begüm , Stadtfeld Matthias , Ohler Uwe , Mahony Shaun , Sanjana Neville E. , Mazzoni Esteban O.
Published: November 2020

In pluripotent cells, a delicate activation-repression balance maintains pro-differentiation genes ready for rapid activation. The identity of transcription factors (TFs) that specifically repress pro-differentiation genes remains obscure. By targeting ~1,700 TFs with CRISPR loss-of-function screen, we found that ZBTB11 and ZFP131 are required for embryonic stem cell (ESC) pluripotency. ZBTB11 and ZFP131 maintain promoter-proximally paused Polymerase II at pro-differentiation genes in ESCs. ZBTB11 or ZFP131 loss leads to NELF pausing factor release, an increase in H3K4me3, and transcriptional upregulation of genes associated with all three germ layers. Together, our results suggest that ZBTB11 and ZFP131 maintain pluripotency by preventing premature expression of pro-differentiation genes and present a generalizable framework to maintain cellular potency.

One-sentence summary

A Transcription Factor-wide CRISPR screen identifies ZBTB11 and ZFP131 maintaining pluripotency by pausing POL II at pro-differentiation genes
Neural signatures of predictive language processing in parkinson’s disease with and without mild cognitive impairment
Authors: León-Cabrera Patricia , Pagonabarraga Javier , Morís Joaquín , Martínez-Horta Saúl , Marín-Lahoz Juan , Horta-Barba Andrea , Bejr-Kasem Helena , Kulisevsky Jaime , Rodríguez-Fornells Antoni
Published: November 2020

Cognitive deficits are common in Parkinson’s disease (PD), with some PD patients meeting criteria for mild cognitive impairment (MCI). An unaddressed question is whether linguistic prediction is preserved in PD. This ability is nowadays deemed crucial in achieving fast and efficient comprehension, and it may be negatively impacted by cognitive deterioration. To fill this gap of knowledge, we used event-related potentials (ERPs) to evaluate mechanisms of linguistic prediction in a sample of PD patients (on dopamine compensation) with and without MCI. To this end, participants read sentence contexts that were predictive or not about a sentence-final word. The final word appeared after 1 second, matching or mismatching the prediction. The introduction of the interval allowed to capture neural responses both before and after sentence-final words, reflecting semantic anticipation and processing. PD patients with normal cognition (N = 58) showed ERP responses comparable to those of matched controls. Specifically, in predictive contexts, a slow negative potential developed prior to sentence-final words, reflecting semantic anticipation. Later, expected words elicited reduced N400 responses (compared to unexpected words), indicating facilitated semantic processing. Besides, PD patients with MCI (N = 20) showed a prolongation of the N400 congruency effect (compared to matched PD patients without MCI), indicating that further cognitive decline impacts semantic processing. Finally, lower verbal fluency scores correlated with prolonged N400 congruency effects and with reduced pre-word differences in all PD patients (N = 78). This relevantly points to a role of deficits in temporal-dependent mechanisms in PD, besides prototypical frontal dysfunction, in altered semantic anticipation and semantic processing during sentence comprehension.
Verticillium dahliaeinoculation andin vitropropagation modify the xylem microbiome and disease reaction to Verticillium wilt in a wild olive genotype
Authors: Anguita-Maeso Manuel , Trapero José Luis , Olivares-García Concepción , Ruano-Rosa David , Palomo-Ríos Elena , Jiménez-Díaz Rafael M. , Navas-Cortés Juan A. , Landa Blanca B.
Published: November 2020

Host resistance is the most practical, long-term and economically efficient disease control measure for Verticillium wilt in olive caused by the xylem-invading fungusVerticillium dahliae(Vd), and it is at the core of the integrated disease management. Plant’s microbiome at the site of infection may have an influence on the host reaction to pathogens; however, the role of xylem microbial communities in the olive resistance toVdhas been overlooked and remain unexplored to date. This research was focused on elucidating whetherin vitroolive propagation may alter the diversity and composition of the xylem-inhabiting microbiome and if those changes may modify the resistance response that a wild olive clone shows to the highly virulent defoliating (D) pathotype ofVd. Results indicated that although there were differences in microbial communities among the different propagation methodologies, most substantial changes occurred when plants were inoculated withVd, regardless whether the infection process took place, with a significant increase in the diversity of bacterial communities when the pathogen was present in the soil. Furthermore, it was noticeable that olive plants multiplied underin vitroconditions developed a susceptible reaction to DVd, characterized by severe wilting symptoms and 100% vascular infection. Moreover, thosein vitropropagated plants showed an altered xylem microbiome with a decrease in total OTU numbers as compared to that of plants multiplied under non-aseptic conditions. Overall, 10 keystone bacterial genera were detected in olive xylem regardless infection byVdand the propagation procedure of plants (in vitrovs nursery), withCutibacterium(36.85%),Pseudomonas(20.93%),Anoxybacillus(6.28%),Staphylococcus(4.95%),Methylobacterium-Methylorubrum(3.91%), andBradyrhizobium(3.54%) being the most abundant.Pseudomonasspp. appeared as the most predominant bacterial group in micropropagated plants andAnoxybacillusappeared as a keystone bacterium inVd-inoculated plants irrespective of their propagation process. Our results are first to show a breakdown of resistance toVdin a wild olive that potentially maybe related to a modification of its xylem microbiome, and will help to expand our knowledge of the role of indigenous xylem microbiome on host resistance which can be of use to fight against main vascular diseases of olive.
The female (XX) and male (YY) genomes provide insights into the sex determination mechanism in spinach
Authors: She Hongbing , Liu Zhiyuan , Xu Zhaosheng , Zhang Helong , Cheng Feng , Wang Xiaowu , Qian Wei
Published: November 2020

Sexual reproduction is the primary means of reproduction for the vast majority of macroscopic organisms, including almost all animals and plants. Sex chromosomes are predicted to play a central role in sexual dimorphism. Sex determination in spinach is controlled by a pair of sex chromosomes. However, the mechanisms of sex determination in spinach remain poorly understand. Here, we assembled the genomes of both a female (XX) and a male (YY) individual of spinach, and the genome sizes were 978 Mb with 28,320 predicted genes and 926 Mb with 26,537 predicted genes, respectively. Based on reported sex-linked markers, chromosomes 4 of the female and male genome were defined as the X and Y chromosomes, and a 10 Mb male-specific region of the Y chromosome (MSY) from approximately 95– 105 Mb, was identified that contains abundant transposable elements (92.32%). Importantly, a large-scale inversion of about 13 Mb in length was detected on the X chromosome, corresponding to ~9 Mb and ~4 Mb on the Y chromosome, which were located on both sides of the MSY with two distinct evolutionary strata. Almost all sex-linked/Y-specific markers were enriched on the inversions/MSY, suggesting that the flanked inversions might result in recombination suppression between the X and Y chromosomes to maintain the MSY. Forty-nine genes within the MSY had functional homologs elsewhere in the autosomal region, suggesting movement of genes onto the MSY. The X and Y chromosomes of spinach provide a valuable resource for investigating spinach sex chromosomes evolution from wild to cultivated spinach and also provide a broader understanding of the sex determination model in the Amaranthaceae family.
Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter
Authors: Osbeck Christofer M.G. , Lundin Daniel , Karlsson Camilla , Teikari Jonna E. , Moran Mary Ann , Pinhassi Jarone
Published: November 2020

Phytoplankton release massive amounts of dissolved organic matter (DOM) into the water column during recurring blooms in coastal waters and inland seas. The released DOM encompasses a complex mixture of both known and unknown compounds, and is a rich nutrient source for heterotrophic bacteria. The metabolic activity of bacteria during and after phytoplankton blooms can hence be expected to reflect the characteristics of the released DOM. We therefore investigated if bacterioplankton could be used as “living sensors” of phytoplankton DOM quantity and/or quality, by applying gene expression analyses to identify bacterial metabolisms induced by DOM. We used transcriptional analysis of two Baltic Sea bacterial isolates (Polaribactersp. BAL334 [Flavobacteriia] andBrevundimonassp. BAL450 [Alphaproteobacteria]) growing with DOM from axenic cultures of the dinoflagellateProrocentrum minimum. We observed pronounced differences between the two bacteria both in bacterial growth and the expressed metabolic pathways in cultures exposed to dinoflagellate DOM compared with controls. Differences in metabolic responses between the two isolates were caused both by differences in gene repertoire between them (e.g. in the SEED categories for membrane transport, motility and photoheterotrophy) and the regulation of expression (e.g. fatty acid metabolism), emphasizing the importance of separating the responses of different taxa in analyses of community sequence data. Similarities between the bacteria included substantially increased expression of genes for Ton and Tol transport systems in both isolates, which are commonly associated with uptake of complex organic molecules.Polaribactersp. BAL334 showed stronger metabolic responses to DOM harvested from exponential than stationary phase dinoflagellates (128 compared to 26 differentially expressed genes), whereasBrevundimonassp. BAL450 responded more to the DOM from stationary than exponential phase dinoflagellates (33 compared to 6 differentially expressed genes). These findings suggest that shifts in bacterial metabolisms during different phases of phytoplankton blooms can be detected in individual bacterial species and can provide insights into their involvement in DOM transformations.
Relationship between serum bilirubin levels, urinary biopyrrin levels, and retinopathy in patients with diabetes
Authors: Kudo Kana , Inoue Tomoaki , Sonoda Noriyuki , Ogawa Yoshihiro , Inoguchi Toyoshi
Published: November 2020

Aims/Introduction

Previous reports have indicated that serum bilirubin levels may be associated with diabetic retinopathy. However, the detailed mechanism is not fully understood. In this study, we evaluated the relationship between the severity of diabetic retinopathy and various factors including bilirubin levels and factors influencing bilirubin metabolism.

Methods

The study participants consisted of 94 consecutive patients with diabetes mellitus admitted to Kyushu University Hospital from April 2011 to July 2012. The patients were classified into three groups: no retinopathy (NDR), simple retinopathy (SDR), and pre-proliferative or proliferative retinopathy (PDR). The relationship between the severity of retinopathy and various factors was evaluated using univariate and logistic regression analyses. In addition, multivariate regression analysis was performed to evaluate the significant determinants for bilirubin levels.

Results

In univariate analysis, a significant difference was found among NDR, SDR and PDR in bilirubin levels, duration of diabetes, systolic blood pressure, and macroalbuminuria. Logistic regression analysis showed that PDR was significantly associated with bilirubin levels, duration of diabetes, and systolic blood pressure (OR 0.737, 95% CI 0.570–0.952, P=0.012; OR 1.085, 95% CI 1.024–1.149, P=0.006; OR 1.036, 95% CI 1.011–1.062, P=0.005, respectively). In turn, multivariate regression analysis showed that bilirubin levels were negatively associated with high-sensitivity Creactive protein levels and PDR, but positively correlated with urinary biopyrrin levels, oxidized metabolites of bilirubin.

Conclusions

PDR was negatively associated with bilirubin levels. This negative association may be due to a decreased production of bilirubin rather than its increased consumption considering the positive association between bilirubin and biopyrrin levels.
Fine-scale population structure reveals high genetic heterogeneity of the Kuwaiti population in the Arabian Peninsula
Authors: Eaaswarkhanth Muthukrishnan , Pathak Ajai K , Ongaro Linda , Montinaro Francesco , Hebbar Prashantha , Alsmadi Osama , Metspalu Mait , Al-Mulla Fahd , Thanaraj Thangavel Alphonse
Published: November 2020

Recent studies have showed the diverse genetic architecture of the highly consanguineous populations inhabiting the Arabian Peninsula. Consanguinity coupled with heterogeneity is complex and makes it difficult to understand the bases of population-specific genetic diseases in the region. Therefore, comprehensive genetic characterization of the populations at the finest scale is warranted. Here, we revisit the genetic structure of the Kuwait population by analyzing genome-wide single nucleotide polymorphisms data from 583 Kuwaiti individuals sorted into three subgroups. We envisage a diverse demographic genetic history among the three subgroups based on drift and allelic sharing with modern and ancient individuals. Furthermore, our comprehensive haplotype-based analyses disclose a high genetic heterogeneity among the Kuwaiti populations. We infer the major sources of ancestry within the newly defined groups; one with an obvious predominance of sub-Saharan/Western Africa mostly comprising Kuwait-B individuals, and other with West Eurasia including Kuwait-P and Kuwait-S individuals. Overall, our results recapitulate the historical population movements and reaffirm the genetic imprints of the legacy of continental trading in the region. Such deciphering of fine-scale population structure and their regional genetic heterogeneity would provide clues to the uncharted areas of disease-gene discovery and related associations in populations inhabiting the Arabian Peninsula.
Bone marrow stromal cell transplantation ameliorates cytopenia caused by depletion FAP-α expressing cells
Authors: Camarillo-Retamosa Eva , Watson Luke , Loftus Paul , Alagesan Senthil , O’Donoghue Yvonne , Deedigan Laura M. , O’Flynn Lisa , Barkley Laura R. , J.Elliman Stephen
Published: November 2020

The marrow microenvironment is a complex and heterogeneous mixture of hematopoietic and stromal progenitors necessary for haematopoiesis. Whilst the hematopoietic progenitors are well described, the stromal cellular composition is not fully elucidated due to the low cells numbers, localisation-distribution-accessibility, and the lack of specific biomarkers. Cellular taxonomy studies have recently identified new populations of stromal subsets with distinct gene signature and regulatory properties of hematopoietic regeneration. Fibroblast activation protein-α (FAP), a stromal cell type first identified in cancer is also rarely found in normal tissues but might play an essential role in tissue homeostasis. Using FAPDM2transgenic mouse in which FAP-expressing cells can be ablated with Diphtheria Toxin (DTX) FAP+cells were depleted in healthy mice. Whilst FAP+cells constituted 5% of all marrow cells; its ablation caused a rapid loss of PDGFR-α, Leptin-R, gp38 and SDC2 stromal cells populations, endothelial cells and vascular disruption. These resulted in anaemia, thrombocytopenia and neutropenia in peripheral blood (PB) and extreme hypo-cellularity in marrow with abnormalities within the hematopoietic progenitors. In an effort to reverse the phenotypes caused by FAP+cell loss, a single intravenous injection of syngeneic bone marrow-derived stromal cells was administered. In a short-term evaluation, anaemia, thrombocytopenia and neutropenia ameliorated in PB and the numbers of marrow hematopoietic progenitors increased. Our data suggest FAP-expressing cells are a non-redundant component of the marrow microenvironment, necessary for marrow homeostasis and haematopoiesis. These data also provided evidence that stromal cell ablation can be rescued by stromal cell therapy.

Significance Statement

FAP-expressing cells depletion led to collateral damage in PB and marrow, including haematological defects that can be ameliorated by adoptive transfer of low-dose,ex-vivoexpanded FAP-expressing marrow stromal cells. We suggest that stromal cell loss is a feature of severe immune-mediated inflammatory diseases – such as Graft versus Host Disease and sepsis - and that FAPDM2model represents a novel tool to explore the native function of the recently identified stromal cell sub-populations.
A ferredoxin bridge connects the two arms of plant mitochondrial complex I
Authors: Klusch Niklas , Senkler Jennifer , Yildiz Özkan , Kühlbrandt Werner , Braun Hans-Peter
Published: November 2020

Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. It is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I fromArabidopsis thalianaand from the green algaPolytomellasp. at 3.2 and 3.3 Å resolution. In both, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved inA. thalianacomplex I, with different angles between the two arms and different conformations of the ND1 loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We suggest that the bridge domain regulates complex I activity.

One sentence summary

The activity of complex I depends on the angel between its two arms, which, in plants, is adjusted by a protein bridge that includes an unusual ferredoxin.
Improve Concentration of Frequency and Time (Conceft) by Novel Complex Spherical Designs
Authors: Sourisseau Matt , Wang Yu Guang , Womersley Robert S. , Wu Hau-Tieng , Yu Wei-Hsuan
Published: November 2020

Abstract

Concentration of frequency and time (ConceFT) is a generalized multitaper algorithm introduced to analyze complicated non-stationary time series. To avoid the randomness in the original ConceFT algorithm, we apply the novel complex spherical design technique to standardize ConceFT, which we coinCQU-ConceFT.The proposed CQU-ConceFT is applied to visualize the spindle structure in the electroencephalogram signal during the N2 sleep stage and other physiological time series.
An equilibrium constant pH molecular dynamics method for accurate prediction of pH-dependence in protein systems: Theory and application
Authors: Kots Ekaterina , Shore Derek M. , Weinstein Harel
Published: November 2020

Computational modeling and simulation of biomolecular systems at their functional pH ranges requires an accurate approach to exploring the pH dependence of conformations and interactions. Here we present a new approach – the Equilibrium Constant pH (ECpH) method – to perform conformational sampling of protein systems in the framework of molecular dynamics simulations in anN, P, T-thermodynamic ensemble. The performance of ECpH is illustrated for two proteins with experimentally determined conformational responses to pH change: the small globular water-soluble bovine b-lactoglobulin (BBL), and the dimer transmembrane antiporter CLC-ec1 Cl−/H+. We show that with computational speeds comparable to equivalent canonical MD simulations we performed, the ECpH trajectories reproduce accurately the pH-dependent conformational changes observed experimentally in these two protein systems, some of which were not seen in the corresponding canonical MD simulations.

Abstract Figure

Table of Contents artwork
Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET
Authors: Peter Martin F. , Gebhardt Christian , Mächtel Rebecca , Glaenzer Janin , Thomas Gavin H. , Cordes Thorben , Hagelueken Gregor
Published: November 2020

Pulsed electron-electron double resonance spectroscopy (PELDOR or DEER) and single molecule Förster resonance energy transfer spectroscopy (smFRET) are recent additions to the toolbox of integrative structural biology. Both methods are frequently used to visualize conformational changes and to determine nanometer-scale distances in biomacromolecules including proteins and nucleic acids. A prerequisite for the application of PELDOR/DEER and smFRET is the presence of suitable spin centers or fluorophores in the target molecule, which are usually introduced via chemical biology methods. The application portfolio of the two methods is overlapping: each allows determination of distances, to monitor distance changes and to visualize conformational heterogeneity and -dynamics. Both methods can provide qualitative information that facilitates mechanistic understanding, for instance on conformational changes, as well as quantitative data for structural modelling. Despite their broad application, a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET is still missing and we set out here to fill this gap. For this purpose, we prepared a library of double cysteine mutants of three well-studied substrate binding proteins that undergo large-scale conformational changes upon ligand binding. The distances between the introduced spin- or fluorescence labels were determined via PELDOR/DEER and smFRET, using established standard experimental protocols and data analysis routines. The experiments were conducted in the presence and absence of the natural ligands to investigate how well the ligand-induced conformational changes could be detected by the two methods. Overall, we found good agreement for the determined distances, yet some surprising inconsistencies occurred. In our set of experiments, we identified the source of discrepancies as the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. Our study highlights strength and weaknesses of both methods and paves the way for a higher confidence in quantitative comparison of PELDOR/DEER and smFRET results in the future.
Short linear motif based interactions and dynamics of the ezrin, radixin, moesin and merlin FERM domains
Authors: Ali Muhammad , Khramushin Alisa , Yadav Vikash K , Schueler-Furman Ora , Ivarsson Ylva
Published: November 2020

The ERM (ezrin, radixin and moesin) family of proteins and the related protein merlin participate in signaling events at the cell cortex. The proteins share an N-terminal FERM (band Four-point-one (4.1) ERM) domain comprised of three subdomains (F1, F2, and F3) that hold multiple binding sites for short linear peptide motifs. By screening the FERM domains of the ERMs and merlin against a phage library that display peptides representing the intrinsically disordered regions of the human proteome we identified more than 220 FERM binding peptides. The majority of the peptides contained an apparent Yx[FILV] motif, but ligands with alternative motifs were also found. Interactions with thirteen peptides were validated using a fluorescence polarization assay, and interactions with seven full-length proteins were validated through pull-down experiments. We investigated the energy landscapes of interactions between the moesin FERM domain and representative set of ligands using Rosetta FlexPepDock computational peptide docking protocols, which provide a detailed molecular understanding of the binding of peptides with distinct motifs (YxV and E[Y/F]xDFYDF) to different sites on the F3 subdomain. A third motif (FY[D/E]L(4-5x)PLxxx[L/V]) was proposed to bind more diffusely. By combining competition and modeling experiments, we further uncovered interdependencies between different types of ligands. The study expands the motif-based interactomes of the ERMs and merlin, and suggests that the FERM domain acts as a switchable interaction hub where one class of ligands to the F3 subdomain allosterically regulates binding of other F3 ligands.
The Drosophila Baramicin polypeptide gene protects against fungal infection
Authors: Hanson M.A. , Cohen L.B. , Marra A. , Iatsenko I. , Wasserman S.A. , Lemaitre B.
Published: November 2020

The fruit flyDrososphila melanogastercombats microbial infection by producing a battery of effector peptides that are secreted into the haemolymph. Technical difficulties prevented the investigation of these short effector genes until the recent advent of the CRISPR/CAS era. As a consequence, many putative immune effectors remain to be characterized and exactly how each of these effectors contributes to survival is not well characterized. Here we describe a novelDrosophilaantifungal peptide gene that we nameBaramicin A. We show thatBaraAencodes a precursor protein cleaved into multiple peptides via furin cleavage sites.BaraAis strongly immune-induced in the fat body downstream of the Toll pathway, but also exhibits expression in the nervous system. Importantly, we show that flies lackingBaraAare viable but susceptible to the enomopathogenic fungusBeauveria bassiana. Consistent withBaraAbeing directly antimicrobial, overexpression ofBaraApromotes resistance to fungi and the IM10-like peptides produced byBaraAsynergistically inhibit growth of fungi in vitro when combined with a membrane-disrupting antifungal. Surprisingly,BaraAmales but not females display an erect wing phenotype upon infection. Collectively, we identify a new antifungal immune effector downstream of Toll signalling, improving our knowledge of theDrosophilaantimicrobial response.
Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis
Authors: Pradhan Saurabh J. , Reddy Puli Chandramouli , Smutny Michael , Sharma Ankita , Sako Keisuke , Oak Meghana S. , Shah Rini , Pal Mrinmoy , Deshpande Ojas , Tang Yin , Mishra Rakesh , Deshpande Girish , Giraldez Antonio J. , Sonawane Mahendra , Heisenberg Carl-Philipp , Galande Sanjeev
Published: November 2020

Zygotic genome activation (ZGA) initiates regionalized transcription responsible for the acquisition of distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, whether the tissue-specific transcription is mechanistically linked with the onset of ZGA is unknown. Here, we have addressed the involvement of chromatin organizer SATB2 in orchestrating these processes during vertebrate embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility revealed contrasting molecular functions of maternal and zygotic pools of Satb2. Maternal Satb2 represses zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented. We discuss the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.
Endogenous p53 expression in human and mouse is not regulated by its 3′UTR
Authors: Mitschka Sibylle , Mayr Christine
Published: November 2020

TheTP53gene encodes the tumor suppressor p53, which is functionally inactivated in many human cancers. Numerous studies found that overexpression of specific microRNAs or RNA-binding proteins can alter p53 expression through binding tocis-regulatory elements in theTP533′ untranslated region (3′UTR). Although these studies suggested that 3′UTR-mediated p53 expression regulation could play a role in tumorigenesis or could be exploited for therapeutic purposes, they did not investigate post-transcriptional regulation of the nativeTP53gene. We used CRISPR/Cas9 to delete the human and mouse p53 3′UTRs while preserving endogenous mRNA processing. This revealed that the endogenous 3′UTR is not involved in regulating p53 mRNA or protein expression neither in steady state nor after genotoxic stress. As we were able to confirm the previously observed repressive effects of the isolated 3′UTR in reporter assays, our data highlight the importance of genetic models in the validation of post-transcriptional gene regulatory effects.
An Examination of an Enhanced Remote Sensing Method for Agent Attribution of Forest Disturbance
Authors: Worsham Hugh Marshall
Published: November 2020

Patterns of disturbance in Sierra Nevada forests are shifting as a result of changing climate and land uses. These changes have underscored the need for a monitoring system that both detects disturbances and attributes them to different agents. Addressing this need will aid forest management and conservation decision-making, potentially enhancing forests’ resilience to changing climatic conditions. In addition, it will advance understanding of the patterns, drivers, and consequences of forest disturbance in space and time. This study proposed and evaluated an enhanced method for disturbance agent attribution. Specifically, it tested the extent to which textural information could improve the performance of an ensemble learning method in predicting the agents of disturbance from remote sensing observations. Random Forest (RF) models were developed to attribute disturbance to three primary agents (fire, harvest, and drought) in Stanislaus National Forest, California, U.S.A., between 1999 and 2015. To account for spectral behavior and topographical characteristics that regulate vegetation and disturbance dynamics, the models were trained on predictors derived from both the Landsat record and from a digital elevation model. The predictors included measurements of spectral change acquired through temporal segmentation of Landsat data; measurements of patch geometry; and a series of landscape texture metrics. The texture metrics were generated using the Grey-Level Co-Occurrence Matrix (GLCM). Two models were produced: one with GLCM texture metrics and one without. The per-class and overall accuracies of each model were evaluated with out-of-bag (OOB) observations and compared statistically to quantify the contribution of texture metrics to classification skill. Overall OOB accuracy was 72.0% for the texture-free model and 72.2% for the texture-dependent model, with no significant accuracy difference between them. Spatial patterns in prediction maps cohered with expectations, with most harvest concentrated in mid-elevation forests and fire and stress co-occurring at lower elevations. Altogether, the method yielded adequate identification of disturbance and moderate attribution accuracy for multiple disturbance agents. While textures did not contribute meaningfully to model skill, the study offers a strong foundation for future development, which should focus on improving the efficacy of the model and generalizing it for systems beyond the Central Sierra Nevada.
HPRep: Quantifying reproducibility in HiChIP and PLAC-seq datasets
Authors: Rosen Jonathan D. , Yang Yuchen , Abnousi Armen , Chen Jiawen , Song Michael , Jones Ian R. , Shen Yin , Hu Ming , Li Yun
Published: November 2020

HiChIP and PLAC-seq are emerging technologies for studying genome-wide long-range chromatin interactions mediated by protein of interest, enabling more sensitive and cost-efficient interrogation of protein-centric chromatin conformation. However, due to the unbalanced read distribution introduced by protein immunoprecipitation, existing reproducibility measures developed for Hi-C data are not appropriate for the analysis of HiChIP and PLAC-seq data.

Here, we present HPRep, a stratified and weighted correlation metric derived from normalized contact counts, to quantify reproducibility in HiChIP and PLAC-seq data. We applied HPRep to multiple real datasets and demonstrate that HPRep outperforms existing reproducibility measures developed for Hi-C data. Specifically, we applied HPRep to H3K4me3 PLAC-seq data from mouse embryonic stem cells and mouse brain tissues, as well as H3K27ac HiChIP data from human lymphoblastoid cell line GM12878 and leukemia cell line K562, showing that HPRep can more clearly separate among pseudo-replicates, real replicates, and non-replicates. Furthermore, in an H3K4me3 PLAC-seq dataset consisting of 11 samples from four human brain cell types, HPRep demonstrates expected clustering of data which could not be achieved by existing methods developed for Hi-C data, highlighting the need of a reproducibility metric tailored to HiChIP and PLAC-seq data.
Membrane-tethered peptides derived from intracellular loops 2 and 3 of the urotensin II receptor act as allosteric biased ligands
Authors: Nassour Hassan , Hoang Tuan Anh , Martin Ryan D. , Dallagnol Juliana C. C. , Billard Étienne , Létourneau Myriam , Novellino Ettore , Carotenuto Alfonso , Allen Bruce G. , Tanny Jason C. , Fournier Alain , Hébert Terence E. , Chatenet David
Published: November 2020

Over the last decade, the urotensinergic system has garnered significant attention as a promising new target for the treatment of various cardiovascular diseases and also cancer. Significant investment toward the development of clinically relevant UT ligands for therapeutic intervention has been made but have met little to no success to date. The UT system, which has yet to be effectively targeted, therefore remains to be therapeutically exploited. The discovery of allosteric sites that allow modulation of receptor activity will increase the searchable chemical space against a disease-relevant target. Pepducins and other lipidated peptides have been used as both mechanistic probes and potential therapeutics. Therefore, pepducins derived from the human urotensin II receptor might represent unique tools to generate signaling bias and study UT signaling networks. Two hUT-derived pepducins, derived from the second and the third intracellular loop of UT, respectively, have been synthesized and pharmacologically characterized. Our results demonstrated that hUT-Pep2 and [Trp1, Leu2]hUT-Pep3 acted as biased ago-allosteric modulators, triggered ERK1/2phosphorylation and to a lesser extent, IP1production, stimulated cell proliferation yet were devoid of contractile activity. Interestingly, both hUT-derived pepducins were able to modulate hUII- and URP-mediated contraction albeit to different extents. These new derivatives represent unique tools to reveal the intricacies of hUT signaling and also a novel avenue to design allosteric ligands selectively targeting UT signaling that could prove to be useful for the treatment of hUT-associated diseases.
Improved SILAC quantification with data independent acquisition to investigate bortezomib-induced protein degradation
Authors: Pino Lindsay K , Baeza Josue , Lauman Richard , Schilling Birgit , Garcia Benjamin A
Published: November 2020

Stable isotope labeling by amino acids in cell culture (SILAC) coupled to data-dependent acquisition (DDA) is a common approach to quantitative proteomics with the desirable benefit of reducing batch effects during sample processing and data acquisition. More recently, using data-independent acquisition (DIA/SWATH) to systematically measure peptides has gained popularity for its comprehensiveness, reproducibility, and accuracy of quantification. The complementary advantages of these two techniques logically suggests combining them. Here, we develop a SILAC-DIA-MS workflow using free, open-source software. We determine empirically that using DIA achieves similar peptide detection numbers as DDA and that DIA improves the quantitative accuracy and precision of SILAC by an order of magnitude. Finally, we apply SILAC-DIA-MS to determine protein turnover rates of cells treated with bortezomib, a 26S proteasome inhibitor FDA-approved for multiple myeloma and mantle cell lymphoma. We observe that SILAC-DIA produces more sensitive protein turnover models. Of the proteins determined differentially degraded by both acquisition methods, we find known ubiquitin-proteasome degrands such as HNRNPK, EIF3A, and IF4A1/EIF4A-1, and a slower turnover for CATD, a protein implicated in invasive breast cancer. With improved quantification from DIA, we anticipate this workflow making SILAC-based experiments like protein turnover more sensitive.
Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc
Authors: Matsuda Shinya , Schaefer Jonas V. , Mii Yusuke , Hori Yutaro , Bieli Dimitri , Taira Masanori , Plückthun Andreas , Affolter Markus
Published: November 2020

How morphogen gradients control patterning and growth in developing tissues remains largely unknown due to lack of tools manipulating morphogen gradients. Here, we generate two membrane-tethered protein binders that manipulate different aspects of Decapentaplegic (Dpp), a morphogen required for overall patterning and growth of the Drosophila wing. “HA trap” is based on a single-chain variable fragment (scFv) against the HA tag that traps HA-Dpp to mainly block its dispersal, while “Dpp trap” is based on a Designed Ankyrin Repeat Protein (DARPin) against Dpp that traps Dpp to block both its dispersal and signaling. Using these tools, we found that, while posterior patterning and growth require Dpp dispersal, anterior patterning and growth largely proceed without Dpp dispersal. We show thatdpptranscriptional refinement from an initially uniform to a localized expression and persistent signaling in transientdppsource cells render the anterior compartment robust against the absence of Dpp dispersal. Furthermore, despite a critical requirement ofdppfor the overall wing growth, neither Dpp dispersal nor direct signaling is critical for lateral wing growth after wing pouch specification. These results challenge the long-standing dogma that Dpp dispersal is strictly required to control and coordinate overall wing patterning and growth.
Spatial correlations and distribution of competence gene expression in biofilms ofStreptococcus mutans
Authors: Ishkov Ivan P. , Kaspar Justin R. , Hagen Stephen J.
Published: November 2020

Streptococcus mutansis an important pathogen in the human oral biofilm. It expresses virulent behaviors that are linked to its genetic competence regulon, which is controlled bycomX. Expression ofcomXis modulated by two diffusible signaling peptides, denoted CSP and XIP, and by other environmental cues such as pH and oxidative stress. The sensitivity ofS. mutanscompetence to environmental inputs that may vary on microscopic length scales raises the question of whether the biofilm environment causes spatial clustering ofS. mutansvirulence behaviors, by creating microniches where competence and related phenotypes are concentrated. We have used two-photon microscopy to characterize the spatial distribution ofcomXexpression among individualS. mutanscells in biofilms. By analyzing correlations incomXactivity, we test for spatial clustering that may suggest localized, competence microenvironments. Our data indicate that both competence-signaling peptides diffuse efficiently through the biofilm. CSP triggers a Poisson-like, spatially random,comXresponse from a subpopulation of cells that is homogeneously dispersed. XIP elicits a population-wide response. Our data indicate that competence microenvironments if they exist are small enough that the phenotypes of individual cells are not clustered or correlated to any greater extent than occurs in planktonic cultures.
Integrating long-range regulatory interactions to predict gene expression using graph convolutional networks
Authors: Bigness Jeremy , Loinaz Xavier , Patel Shalin , Larschan Erica , Singh Ritambhara
Published: November 2020

Long-range spatial interactions among genomic regions are critical for regulating gene expression, and their disruption has been associated with a host of diseases. However, when modeling the effects of regulatory factors, most deep learning models either neglect long-range interactions or fail to capture the inherent 3D structure of the underlying genomic organization. To address these limitations, we present GC-MERGE, aGraphConvolutionalModel forEpigeneticRegulation ofGeneExpression. Using a graph-based framework, the model incorporates important information about long-range interactions via a natural encoding of spatial interactions into the graph representation. It integrates measurements of both the spatial genomic organization and local regulatory factors, specifically histone modifications, to not only predict the expression of a given gene of interest but also quantify the importance of its regulatory factors. We apply GC-MERGE to datasets for three cell lines - GM12878 (lymphoblastoid), K562 (myelogenous leukemia), and HUVEC (human umbilical vein endothelial) - and demonstrate its state-of-the-art predictive performance. Crucially, we show that our model is interpretable in terms of the observed biological regulatory factors, high-lighting both the histone modifications and the interacting genomic regions contributing to a gene’s predicted expression. We provide model explanations for multiple exemplar genes and validate them with evidence from the literature. Our model presents a novel setup for predicting gene expression by integrating multimodal datasets in a graph convolutional framework. More importantly, it enables interpretation of the biological mechanisms driving the model’s predictions. Available at:https://github.com/rsinghlab/GC-MERGE.
DNA barcodes and reliable molecular identifications in a diverse group of invasive pests: lessons fromBactrocerafruit flies on variation across the COI gene, introgression, and standardization
Authors: Doorenweerd Camiel , Jose Michael San , Leblanc Luc , Barr Norman , Geib Scott , Chung Arthur Y.C. , Dupuis Julian , Ekayanti Arni , Fiegalan Elaida R. , Hemachandra K.S. , Hossain M. Aftab , Huang Chia-Lung , Hsu Yu-Feng , Morris Kimberly Y. , Mustapeng Andi Maryani , Niogret Jerome , Pham Thai Hong , Sirisena U.G.A.I. , Rubinoff Daniel
Published: November 2020

The utility of a universal DNA ‘barcode’ fragment of 658 base pairs of theCytochrome C Oxidase I(COI) gene for the recognition of all animal species has been a widely debated topic on theoretical and practical levels. Regardless of its challenges, large amounts of COI sequence data have been produced in the last two decades. To optimally use the data towards reliable species identification will require further steps to validate the method and reference libraries. The fruit fly tribe Dacini holds about a thousand species, of which eighty are pests of economic concern, including some of the world’s foremost fruit and vegetable pests, and there are many morphologically cryptic species complexes in the tribe. Where previous studies showed limited success in using COI to identify Dacini, our results with a highly curated morphological dataset indicate high congruence between morphology and COI: 90% of the species in our 5,576 sequences, 262-species global dataset can be identified with COI alone based on a monophyly criterion. However, in some key pest species belonging to complexes that were previously thought diagnosable with COI, we found that expanded sampling and independent validation of identifications using genomic data revealed introgression of mitochondrial DNA. We find that the informative SNPs are uniformly distributed across the COI gene, and we provide recommendations for standardization. We conclude that reliable molecular identifications with COI require extensive species coverage, population sampling, and genomics-supported reference identifications before they can be validated as a “diagnostic” marker for specific groups.
Enteric glial cells respond to a dietary change in the lamina propria in a MyD88-dependent manner
Authors: Liu Zhuanzhuan , Sun Hongxiang , Liang Ming , Gao Jing , Meng Liyuan , Zheng Xingping , Wei Yanxia , Kou Yanbo , Wang Yugang
Published: November 2020

Immune and nervous system sensing are two important ways of detecting inner and outer environmental changes. Immune cell activation in the gut can promote metabolic disorders. However, whether enteric nervous system sensing and activities are also important in metabolic syndromes is not clear. Enteric glial cells (EGCs) are thought to have sensing ability, but little is known about the potential connections between EGC and metabolic disorders. Consuming a modern Western-type high-fat low-fiber diet increases the risk of obesity. Here, we reported that dietary shift from a normal chow diet to a high-fat diet in wild-type (WT) C57BL/6 mice induced a transient emergence of glial fibrillary acidic protein (GFAP)-positive EGC network in the ileal lamina propria, accompanied by an increase of glial-derived neurotrophic factors production. Inhibition of EGC metabolic activity via gliotoxin fluorocitrate or glial-intrinsic deletion of myeloid differentiation factor 88 (Myd88) in mice blocked this dietary change-induced activity. Furthermore, we found a different role of MYD88 in glial cells versus adipocyte in diet-induced obesity. The glialMyd88knockout mice gained less body weight after HFD feeding compared to the littermate controls. In contrast, adipocyte deletion ofMyd88in mice had no impact on the weight gain but had exacerbated glucose metabolic disorders. Pharmacological interventions of glial activities by fluorocitrate prevented body weight gain in a dietary type- and glial MYD88-independent manner. Collectively, our data reveal a previously unappreciated function of EGC in sensing a dietary shift-induced perturbation and glial activities as a whole may play roles in diet-induced obesity.

New & Noteworthy

It is known that obesity and its related metabolic syndrome can damage the neuronal system. However, whether the neuronal system also participates in the development of obesity is unclear. Diet is an important contributing factor to obesity. Our study reveals that consuming a high-fat diet can induce a transient enteric glial cell response via its intrinsic sensing molecule(s). Inhibiting overall glial cell activities may have an impact on the development of the metabolic syndrome.