bluuebunny/crossref_metadata_2025 huggingface dataset:
Cost-effectiveness of internet-delivered cognitive behaviour therapy for body dysmorphic disorder: results from a randomised controlled trial
Authors: Flygare Oskar , Andersson Erik , Glimsdal Gjermund , Mataix-Cols David , Djurfeldt Diana , Rück Christian , Enander Jesper
Published: August 2021

Objectives

To evaluate the cost-effectiveness of internet-delivered cognitive behaviour therapy for body dysmorphic disorder (BDD-NET).

Design

Secondary cost-effectiveness analysis from a randomised controlled trial on BDD-NET versus online supportive psychotherapy.

Setting

Academic medical centre.

Participants

Self-referred adult patients with a primary diagnosis of body dysmorphic disorder and a score of 20 or higher on the modified Yale-Brown obsessive compulsive scale (n = 94). Patients receiving concurrent psychotropic drug treatment were included if the dose had been stable for at least two months and remained unchanged during the trial.

Interventions

Participants received either BDD-NET (n = 47) or online supportive psychotherapy (n = 47) for 12 weeks.

Primary and secondary outcome measures

The primary outcome measures were cost-effectiveness and cost-utility from a societal perspective, using remission status from a diagnostic interview and quality-adjusted life years from EQ-5D, respectively. Secondary outcome measures were cost-effectiveness and cost-utility from a health care perspective and the clinic’s perspective.

Results

Compared to supportive psychotherapy, BDD-NET produced one additional remission for an average societal cost of $4132. The cost-utility analysis showed that BDD-NET generated one additional QALY to an average cost of $14319 from a societal perspective.

Conclusions

BDD-NET is a cost-effective treatment for body dysmorphic disorder, compared to online supportive psychotherapy. The efficacy and cost-effectiveness of BDD-NET should be directly compared to face-to-face cognitive behaviour therapy.

Trial registration

NCT02010619

Strengths and limitations of this study

This is the first cost-effectiveness evaluation of a novel internet-delivered treatment designed to increase access to cognitive behaviour therapy for patients with body dysmorphic disorder

Cost estimations were self-rated and might not capture all costs associated with treatment

The self-referred participants were likely motivated to undergo treatment.
Asymmetric depth-filtration – a versatile and scalable approach for isolation and purification of extracellular vesicles
Authors: Chernyshev Vasiliy S. , Chuprov-Netochin Roman N. , Tsydenzhapova Ekaterina , Svirshchevskaya Elena V. , Poltavtseva Rimma A. , Merdalimova Anastasiia , Yashchenok Alexey , Keshelava Amiran , Sorokin Konstantin , Keshelava Varlam , Sukhikh Gennadiy T. , Gorin Dmitry , Leonov Sergey , Skliar Mikhail
Published: August 2021

A novel asymmetric depth filtration (DF) approach for isolation of extracellular vesicles (EVs) from biological fluids is presented, and its performance is compared with established methods. The developed workflow is simple, inexpensive, and relatively fast. Compared with ultracentrifugation and size-exclusion chromatography, the developed method isolates EVs with higher purity and yield. Only standard laboratory equipment is needed for its implementation, which makes it suitable for low-resource locations. The described implementation of the method is suitable for EV isolation from small biological samples in diagnostic and treatment guidance applications. Following the scale-up routes adopted in the biomanufacturing of therapeutics, which routinely rely on DF as one of the product purification steps, the developed method may be scaled up to harvesting therapeutic EVs from large volumes of growth medium.
Spectral fiber-photometry derives hemoglobin concentration changes for accurate measurement of fluorescent sensor activity
Authors: Zhang Wei-Ting , Chao Tzu-Hao Harry , Yang Yue , Wang Tzu-Wen , Lee Sung-Ho , Oyarzabal Esteban A. , Zhou Jingheng , Nonneman Randy , Pegard Nicolas C. , Zhu Hongtu , Cui Guohong , Shih Yen-Yu Ian
Published: August 2021

Fiber-photometry is an emerging technique for recording fluorescent sensor activity in the brain. However, significant hemoglobin-absorption artifacts in fiber-photometry data may be misinterpreted as sensor activity changes. Because hemoglobin exists in nearly every location in the brain and its concentration varies over time, such artifacts could impede the accuracy of many photometry recording results. Here we present a novel use of spectral photometry technique and propose computational methods to quantify photon absorption effects by using activity-independent fluorescence signals, which can be used to derive oxy- and deoxy-hemoglobin concentration changes. Following time-locked neuronal activationin vivo, we observed that a 20% increase in CBV contributes to about a 4% decrease in green fluorescence signal and a 2% decrease in red fluorescence signal. While these hemoglobin concentration changes are often temporally delayed than the fast-responding fluorescence spikes, we found that erroneous interpretation may occur when examining pharmacology-induced sustained activity changes, and in some cases, hemoglobin-absorption could flip the GCaMP signal polarity. We provided hemoglobin-based correction methods to restore fluorescence signals across spectra and compare our results against the commonly used regression approach. We also demonstrated the utility of spectral fiber-photometry for delineating brain regional differences in hemodynamic response functions.

Highlights

Hemoglobin-absorption compromises fiber-photometry recordingin vivo

Spectral photometry allows quantification of hemoglobin concentration changes for correction

The proposed platform allows measuring regional differences in neurovascular transfer function
Engineering a dynamic, controllable infectivity switch in bacteriophage T7
Authors: Chitboonthavisuk Chutikarn , Luo Chun Huai , Huss Phil , Fernholz Mikayla , Raman Srivatsan
Published: August 2021

Transcriptional repressors play an important role in regulating phage genomes. Here, we examined how synthetic regulation based on repressors can be to create a dynamic, controllable infectivity switch in bacteriophage T7. We engineered T7 by replacing a large region of the early phage genome with combinations of ligand-responsive promoters and ribosome binding sites (RBS) designed to control the phage RNA polymerase. Phages with the engineered switch showed virulence comparable to wildtype when not repressed, indicating the phage can be engineered without a loss of fitness. When repressed, the most effective switch used a TetR promoter and a weak RBS, resulting in a two-fold increase in latent period (time to lyse host) and change in phage titer. Further, phage activity could be tuned by varying inducer concentrations. Our study provides a proof of concept for a simple circuit for user control over phage infectivity.
Information Flow in the Fibroblast Growth Factor Receptor Communication Channel
Authors: Díaz José , Martínez-Mekler Gustavo
Published: August 2021

In this work we analyze the flow of information through the Fibroblast Growth Factor Receptor (FGFR) communication channel when different types of signals are transmitted by the MAPK cascade to the gene regulatory network (GRN) formed by the genes C-Myc, DUSP, and Cdc25A, which control fibroblast proliferation. We used the canonical mathematical model of the MAPK cascade coupled to a stochastic model for the activation of the gene regulatory network, subject to different types of FGF inputs (step, quadratic pulses, Dirac delta, and white noise), in order to analyze the response of the gene regulatory network to each type of signal, and determine the temporal variation of the value of its Shannon entropy in each case. Our model suggests that the sustained activation of the FGFR communication channel with a step of FGF > 1 nM is required for cell cycle progression and that during the G1/S transition the amount of uncertainty of the GRN remains at a steady value of ∼ 2.75 bits, indicating that while the fibroblast stimulation with FGF continues the G1/S transition does not require an additional interchange of information between the emitter and the gene regulatory network to be completed. We also found that either low frequency pulses of FGF or low frequency noise, both with a frequency f ≤ 2.77 Hz, are not filtered by the MAPK cascade and can modify the output of the communication channel, i.e., the amount of the effector proteins c-myc, cdc25A and DUSP. An additional effect suggested by our model is that o low frequency periodic signals and noise possibly blockage cell cycle progression because the threshold value concentration of cdc25A for the G1/S transition is not sustained in the in the nucleus during the 10 hours that this process lasts. Finally, from our model we can estimate the capacity of this communication channel in 0.96 bits/min.
PU.1 and MYC transcriptional network defines synergistic drug responses to KIT and LSD1 inhibition in acute myeloid leukemia
Authors: Smith Brittany M. , VanCampen Jake , Kong Garth L. , Yashar William , Tsang Yiu H. , Horton Wesley , Coleman Daniel J. , Estabrook Joseph , Lusardi Theresa A. , Mills Gordon B. , Druker Brian J. , Maxson Julia E. , Braun Theodore P.
Published: August 2021

Activating mutations in the KIT tyrosine receptor kinase confer an adverse prognosis for patients with acute myeloid leukemia (AML). Outside of bone marrow transplantation, treatment options are limited. Here we demonstrate combined KIT and LSD1 inhibition produces synergistic cell death against KIT mutant AML cells. This combination suppresses MYC expression to drive cell cycle exit and apoptosis. This decreased MYC expression results from a loss of PU.1 binding at downstream MYC enhancers. The drug combination also inactivates PI3K/AKT/GSK3a/b signaling to decrease MYC protein abundance. KIT-mutant AML cells rapidly adapt to KIT inhibitor monotherapy by restoring PI3K/AKT activity, but cannot when treated with combined KIT and LSD1 inhibitor. In addition, we validate MYC suppression as a mechanism of synergy in KIT-mutant AML patient samples. Collectively, this work provides rational for a clinical trial to assess the efficacy of KIT and LSD1 inhibition in patients with KIT-mutant AML.

Statement of significance

Effective treatment options for AML are limited. We describe the synergistic response to combined KIT and LSD1 inhibition in KIT-mutant AML and identify key biomarkers of drug response. The specificity and efficacy of this combination in cell lines and patient samples provides rationale for investigation in early phase clinical trials.
Defining dysfunction due to loss of MECP2 in Rett Patient Brain
Authors: Korsakova E , Morales A , McDaniel T , Lund A , Cooper B , Ma F , Allison TF , Plath K , Graham NA , Bhaduri A , Lowry WE
Published: August 2021

Rett Syndrome is characterized by a postnatal loss of neurophysiological function and regression of childhood development. Because the syndrome is X-linked and males with MECP2 mutations generally do not survive birth, the study of this syndrome has been complicated by the fact that in female brain, a portion of neurons express wild type MECP2, and another portion express a non-functional allele of MECP2. Therefore, bulk-RNA-sequencing of Rett brain is confounded by the presence of chimerism of neurons for functional MECP2 in neurons. We developed an approach that allows for single-nuclei transcriptional profiling of individual neurons and a direct comparison between neurons that express functional MECP2 with those that express the disease-causing allele. We found that mutant neurons from Rett brain show patterns of aberrant expression of synaptic and metabolic genes, both of which can be detected in in vitro models of Rett Syndrome. We used these resources to identify a role for POU2F1/OCT1 transcription factor in mediating the response to stress due to loss of MECP2, highlighting a potential key molecular regulator of stress in Rett neurons. Together, our new sorting approach enables us to highlight defective molecular and metabolic pathways in Rett brain neurons and suggests that in vitro models could serve as valuable tools to further study this syndrome and potentially for development of novel therapeutics.
Brominated Lipid Probes Expose Structural Asymmetries in Constricted Membranes
Authors: Moss Frank R. , Lincoff James , Tucker Maxwell , Mohammed Arshad , Grabe Michael , Frost Adam
Published: August 2021

Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane remodeling system, we observed leaflet-level and protein-localized lipid structural patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates, and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated SDPC showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl (DHA) tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.

One-Sentence Summary

Cryo-EM imaging of halogenated lipids and MD simulations provide molecular-scale insight into constricted bilayer structure.
Defective ORF8 dimerization in delta variant of SARS CoV2 leads to abrogation of ORF8 MHC-I interaction and overcome suppression of adaptive immune response
Authors: Chaudhari Armi M , Singh Indra , Joshi Madhvi , Patel Amrutlal , Joshi Chaitanya
Published: August 2021

In India, the breakthrough infections during second wave of COVID-19 pandemic was due to SARS-COV-2 delta variant (B.1.617.2). It was reported that majority of the infections were caused by the delta variant and only 9.8% percent cases required hospitalization whereas, only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections was observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Down regulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant results in structural instability of ORF8 dimer caused by disruption of hydrogen bonding and salt bridges as revealed by structural analysis and MD simulation studies of ORF8 dimer. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 may not hindering the MHC-I expression thereby resulting in better immune response against SARS-CoV-2 delta variant, which partly explains the sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India

Graphical Abstract
Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export
Authors: Duan Lauren , Zaepfel Benjamin L. , Aksenova Vasilisa , Dasso Mary , Rothstein Jeffrey D. , Kalab Petr , Hayes Lindsey R.
Published: August 2021

Nuclear clearance of the DNA/RNA-binding protein TDP-43 is a pathologic hallmark of amyotrophic lateral sclerosis and frontotemporal dementia that remains unexplained. Moreover, our current understanding of TDP-43 nucleocytoplasmic shuttling does not fully explain the predominantly nuclear localization of TDP-43 in healthy cells. Here, we used permeabilized and live-cell models to investigate TDP-43 nuclear export and the role of RNA in TDP-43 localization. We show that TDP-43 nuclear efflux occurs in low-ATP conditions and independent of active mRNA export, consistent with export by passive diffusion through nuclear pore channels. TDP-43 nuclear residence requires binding to GU-rich nuclear intronic pre-mRNAs, based on the induction of TDP-43 nuclear efflux by RNase and GU-rich oligomers and TDP-43 nuclear retention conferred by pre-mRNA splicing inhibitors. Mutation of TDP-43 RNA recognition motifs disrupts TDP-43 nuclear accumulation and abolishes transcriptional blockade-induced TDP-43 nuclear efflux, demonstrating strict dependence of TDP-43 nuclear localization on RNA binding. Thus, the nuclear abundance of GU-rich intronic pre-mRNAs, as dictated by the balance of transcription and pre-mRNA processing, regulates TDP-43 nuclear sequestration and availability for passive nuclear export.
Presence of multiple parasitoids decreases host survival under warming, but parasitoid performance also decreases
Authors: Thierry Mélanie , Pardikes Nicholas A. , Rosenbaum Benjamin , Ximénez-Embún Miguel G. , Hrček Jan
Published: August 2021

Current global changes are reshaping ecological communities and modifying environmental conditions. We need to recognize the combined impact of these biotic and abiotic factors on species interactions, community dynamics, and ecosystem functioning. Specifically, the strength of predator-prey interactions often depends on the presence of other natural enemies: it weakens with competition and interference or strengthens with facilitation. Such effects of multiple predators on prey are likely to be affected by changes in the abiotic environment, altering top-down control, a key structuring force in natural and agricultural ecosystems. Here, we investigated how warming alters the effects of multiple predators on prey suppression using a dynamic model coupled with empirical laboratory experiments withDrosophila-parasitoid communities. While multiple parasitoids enhanced top-down control under warming, parasitoid performance generally declined when another parasitoid was present due to competitive interactions. This could reduce top-down control over multiple generations. Our study highlights the importance of accounting for interactive effects between abiotic and biotic factors to better predict community dynamics in a rapidly changing world and thus better preserve ecosystem functioning and services such as biological control.
Mean-field theory accurately captures the variation of copy number distributions across the mRNA’s life cycle
Authors: Szavits-Nossan Juraj , Grima Ramon
Published: August 2021

We consider a stochastic model where a gene switches between two states, an mRNA transcript is released in the active state and subsequently it undergoes an arbitrary number of sequential unimolecular steps before being degraded. The reactions effectively describe various stages of the mRNA life cycle such as initiation, elongation, termination, splicing, export and degradation. We construct a novel mean-field approach that leads to closed-form steady-state distributions for the number of transcript molecules at each stage of the mRNA life cycle. By comparison with stochastic simulations, we show that the approximation is highly accurate over all of parameter space, independent of the type of expression (constitutive or bursty) and of the shape of the distribution (unimodal, bimodal and nearly bimodal). The theory predicts that in a population of identical cells, any bimodality is gradually washed away as the mRNA progresses through its life cycle.
MEOX2 homeobox gene promotes growth of malignant gliomas
Authors: Schönrock Anna , Heinzelmann Elisa , Steffl Bianca , Narayanan Ashwin , Krunic Damir , Bähr Marion , Park Jong-Whi , Schmidt Claudia , Özduman Koray , Pamir M. Necmettin , Wick Wolfgang , Bestvater Felix , Weichenhan Dieter , Plass Christoph , Taranda Julian , Mall Moritz , Turcan Şevin
Published: August 2021

Glioblastoma (GBM) is an aggressive tumor that frequently exhibits gain of chromosome 7, loss of chromosome 10 and aberrantly activated receptor tyrosine kinase signaling pathways. Here, we identify mesenchyme homeobox 2 (MEOX2) on chromosome 7 with increased expression in GBM as a salient oncogenic transcription factor. Specifically, we show that MEOX2 overexpression leads to increased ERK phosphorylation, and we identify a phosphorylation site on MEOX2 that regulates its transcriptional activity by altering its subnuclear localization. We show that MEOX2 overexpression can lead to increased growth in GBM implantation models and cooperates with loss of p53 and PTEN in cerebral organoid models of human malignant gliomas to induce cell proliferation. Furthermore, using high-throughput genomics, we identify transcriptional target genes of MEOX2 in patient-derived GBM tumorsphere models and a fresh frozen GBM tumor. These analyses show that MEOX2 activates several oncogenic pathways involved in MAPK signaling and extracellular matrix organization. Furthermore, MEOX2 binds to oncogenic ETS factors and known glioma oncogenes such as FABP7. In total, we reveal a novel role for MEOX2 in GBM initiation and progression and demonstrate that MEOX2 can enhance ERK signaling through a feed-forward mechanism.

Significance Statement

Glioblastoma (GBM) harbors gain of chromosome 7 as an early driver event. In this study, we show that mesenchyme homeobox 2 (MEOX2), an aberrantly upregulated transcription factor on chromosome 7, is an oncogene in human glioblastoma. In contrast to GBM, MEOX2 expression is very low in normal brain. We show that MEOX2 cooperates with p53 and PTEN loss to promote tumor initiation in cerebral organoid models. In addition, we identify direct and indirect molecular targets of MEOX2 and demonstrate its role in activating the ERK signaling cascade. These findings identify a novel oncogene in GBM and highlight the transcriptional networks hijacked by these tumors to activate signaling pathways central to GBM biology.
Comparing surrogates to evaluate precisely timed higher-order spike correlations
Authors: Stella Alessandra , Bouss Peter , Palm Günther , Grün Sonja
Published: August 2021

The generation of surrogate data, i.e., the modification of original data to destroy a certain feature, is used for the implementation of a null-hypothesis whenever an analytical approach is not feasible. Thus, surrogate data generation has been extensively used to assess the significance of spike correlations in parallel spike trains. In this context, one of the main challenges is to properly construct the desired null-hypothesis distribution and to avoid a bias in the null-hypothesis by altering the spike train statistics.

A classical surrogate technique is uniform dithering (UD), which displaces spikes locally and uniformly. In this study, we compare UD against five surrogate techniques (two newly introduced) in the context of the detection of significant spatio-temporal spike patterns. We evaluate the surrogates for their performance, first on spike trains based on point process models with constant firing rate, and second on modeled non-stationary artificial data serving as ground truth to assess the pattern detection in a more complex and realistic setting. We determine which statistical features of the original spike trains are modified and to which extent. Moreover, we find that UD fails as an appropriate surrogate because it leads to a loss of spikes in the context of binning and clipping, and thus to a large number of false-positive patterns. The other surrogates achieve a better performance in detecting precisely timed higher-order correlations. Based on these insights, we analyze experimental data from pre-/motor cortex of macaque monkeys during a reaching-and-grasping task for spatio-temporal spike patterns.

Significance statement

Temporal jittering or dithering of single spikes or subsections of spike trains is a common method of generating surrogate data for the statistical analysis of temporal spike correlations. We discovered a serious problem with the classical and widely used method of uniform dithering that can lead to an overestimation of significance, i.e., to false positives in the statistical evaluation of spatio-temporal spike patterns. Therefore we consider 5 other dithering methods, compare and evaluate their statistical properties. Finally, we apply a much better method (trial shifting) to the analysis of experimental multiple-unit recordings and find several highly significant patterns that also reflect different experimental situations.
Differential Analysis of RNA Structure Probing Experiments at Nucleotide Resolution: Uncovering Regulatory Functions of RNA Structure
Authors: Yu Bo , Li Pan , Zhang Qiangfeng Cliff , Hou Lin
Published: August 2021

RNAs perform their function by forming specific structures, which can change across cellular conditions. Structure probing experiments combined with next generation sequencing technology have enabled transcriptome-wide analysis of RNA secondary structure in various cellular conditions. Differential analysis of structure probing data in different conditions can reveal the RNA structurally variable regions (SVRs), which is important for understanding RNA functions. Here, we propose DiffScan, a computational framework for normalization and differential analysis of structure probing data in high resolution. DiffScan preprocesses structure probing datasets to remove systematic bias, and then scans the transcripts to identify SVRs and adaptively determines their lengths and locations. The proposed approach is compatible with most structure probing platforms (e.g., icSHAPE, DMS-seq). When evaluated with simulated and benchmark datasets, DiffScan identifies structurally variable regions at nucleotide resolution, with substantial improvement in accuracy compared with existing SVR detection methods. Moreover, the improvement is robust when tested in multiple structure probing platforms. Application of DiffScan in a dataset of multi-subcellular RNA structurome identified multiple regions that form different structures in nucleus and cytoplasm, linking RNA structural variation to regulation of mRNAs encoding mitochondria-associated proteins. This work provides an effective tool for differential analysis of RNA secondary structure, reinforcing the power of structure probing experiments in deciphering the dynamic RNA structurome.
Electrochemical Detection of Adrenaline and Hydrogen Peroxide on Carbon Nanotube Electrodes
Authors: Khot Gaurang , Kaboli Mohsen , Celikel Tansu , Shirtcliffe Neil
Published: August 2021

Adrenaline and hydrogen peroxide have neuromodulatory functions in the brain. Considerable interest exists in developing electrochemical sensors that can detect their levels in vivo due to their important biochemical roles. Challenges associated with electrochemical detection of hydrogen peroxide and adrenaline are that the oxidation of these molecules usually requires highly oxidising potentials (beyond 1.4 V vs Ag/AgCl) where electrode damage and biofouling are likely and the signals of adrenaline, hydrogen peroide and adenosine overlap. To address these issues we fabricated pyrolysed carbon electrodes coated with oxidised carbon nanotubes (CNTs). Using these electrodes for fast-scan cyclic voltammetric (FSCV) measurements showed that the electrode offers reduced overpotentials compared with graphite and improved resistance to biofouling. The Adrenaline peak is reached at 0.75(±0.1) V and reduced back at -0.2(±0.1) V while hydrogen peroxide is detected at 0.85(±0.1) V on this electrode. The electrodes are highly sensitive with a sensitivity of 16nA µM-1 for Adrenaline and 11nA µM-1 for hydrogen peroxide on an 80 µm2 electrode. They are also suitable to distinguish between adrenaline, hydrogen peroxide and adenosine thus these probes can be used for multimodal detection of analytes.
Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter
Authors: Mourkas Evangelos , Yahara Koji , Bayliss Sion C. , Calland Jessica K. , Johansson Håkan , Mageiros Leonardos , Muñoz-Ramirez Zilia Y. , Futcher Grant , Méric Guillaume , Hitchings Matthew D. , Sandoval-Motta Santiago , Torres Javier , Jolley Keith A. , Maiden Martin C. J. , Ellström Patrik , Waldenström Jonas , Pascoe Ben , Sheppard Samuel K.
Published: August 2021

Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter there are species with divergent ecologies, from rarely isolated single host specialists to multi-host generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterising these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analysing recipient and donor population ancestry among genomes from 30 Campylobacter species we show that cohabitation in the same host can lead to a 6-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.
Regulation of ammonium acquisition and use in Oryza longistaminata ramets under nitrogen source heterogeneity
Authors: Kawai Misato , Tabata Ryo , Ohashi Miwa , Honda Haruno , Kamiya Takehiro , Kojima Mikiko , Takebayashi Yumiko , Oishi Shunsuke , Okamoto Satoru , Hachiya Takushi , Sakakibara Hitoshi
Published: August 2021

Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We studied the response of ramet pairs to heterogeneous nitrogen availability by using a split hydroponic system that allowed each ramet root to be exposed to different conditions. Ammonium uptake was compensatively enhanced in the sufficient-side root when roots of the ramet pairs were exposed to ammonium-sufficient and deficient conditions. Comparative transcriptome analysis revealed that a gene regulatory network for effective ammonium assimilation and amino acid biosynthesis was activated in the sufficient-side roots. Allocation of absorbed nitrogen from the nitrogen-sufficient to the deficient ramets was rather limited. Nitrogen was preferentially used for newly growing axillary buds on the sufficient-side ramets. Biosynthesis of trans-zeatin, a cytokinin, was up-regulated in response to the nitrogen supply, but trans-zeatin appears not to target the compensatory regulation. Our results also implied that the O. longistaminata ortholog of OsCEP1 plays a role as a nitrogen-deficient signal in inter-ramet communication, providing compensatory up-regulation of nitrogen assimilatory genes. These results provide insights into the molecular basis for efficient growth strategies of asexually proliferating plants growing in areas where the distribution of ammonium ions is spatially heterogeneous.

One sentence summary

Oryza longistaminata, a rhizomatous wild rice, systemically regulates ammonium acquisition and use in response to spatially heterogeneous nitrogen availability via inter-ramet communication.
CULTURE AND MAINTENANCE OF URINE-DERIVED, 3-DIMENSIONAL CANINE TRANSITIONAL CELL CARCINOMA ORGANOIDS
Authors: Thenuwara Savantha , Schneider Ben , Mosichuk Allison , Gabriel Vojtech , Zdyrski Christopher , Dao Kimberly , Iennarella-Servantez Chelsea , Colosimo Madeline , Sahoo Dipak , Bourgois-Mochel Agnes , Palerme Jean-Sebastien , Musser Margaret , Johannes Chad , Allenspach Karin , Mochel Jonathan P.
Published: August 2021

Bladder cancer is the ninth most common malignancy in the world. Transitional cell carcinoma (TCC), also referred to as urothelial carcinoma (UC) is the most common form of bladder cancer, occurring in 90% of cases. In this study, we explore urine-derived, 3-dimensional, canine TCC organoids as a possible model to study bladder TCC ex vivo. After establishing the cell lines, we subjected the 3D cells to RNA in situ hybridization (RNA-ISH) and cell viability assays. Overall, 3D cell culture from urine samples of TCC diagnosed canines expressed RNA biomarkers in a similar manner to parent tumors via RNA-ISH and showed more sensitivity to cisplatin treatment when compared to 2D human TCC cells. With further experimentation, canine TCC organoids could become an ideal model to study TCC ex vivo.
Linking ecological specialization to its macroevolutionary consequences: An example with passerine nest type
Authors: Zenil-Ferguson Rosana , McEntee Jay P. , Burleigh J. Gordon , Duckworth Renée A.
Published: August 2021

A long-standing hypothesis in evolutionary biology is that the evolution of resource specialization can lead to an evolutionary dead end, where specialists have low diversification rates and limited ability to evolve into generalists. In recent years, advances in comparative methods investigating trait-based differences associated with diversification have enabled more robust tests of this idea and have found mixed support. We test the evolutionary dead end hypothesis by estimating net diversification rate differences associated with nest type specialization among 3,224 species of passerine birds. In particular, we test whether the adoption of hole-nesting, a nest type specialization that decreases predation, results in reduced diversification rates relative to nesting outside of holes. Further, we examine whether evolutionary transitions to the specialist hole-nesting state have been more frequent than transitions out of hole-nesting. Using diversification models that accounted for background rate heterogeneity and different extinction rate scenarios, we found that hole-nesting specialization was not associated with diversification rate differences. Furthermore, contrary to the assumption that specialists rarely evolve into generalists, we found that transitions out of hole-nesting occur more frequently than transitions into hole-nesting. These results suggest that interspecific competition may limit adoption of hole-nesting, but that such competition does not result in limited diversification of hole-nesters. In conjunction with other recent studies using robust comparative methods, our results add to growing evidence that evolutionary dead ends are not a typical outcome of resource specialization.
Mismatch repair deficiency is not sufficient to increase tumor immunogenicity
Authors: Westcott Peter M K , Muyas Francesc , Smith Olivia , Hauck Haley , Sacks Nathan J , Ely Zackery A , Jaeger Alex M , Rideout William M , Bhutkar Arjun , Zhang Daniel , Beytagh Mary C , Canner David A , Bronson Roderick T , Naranjo Santiago , Jin Abbey , Patten JJ , Cruz Amanda M , Cortes-Ciriano Isidro , Jacks Tyler
Published: August 2021

DNA mismatch repair deficiency (MMRd) in human cancer is associated with high tumor mutational burden (TMB), frameshift mutation-derived neoantigens, increased T cell infiltration, and remarkable responsiveness to immune checkpoint blockade (ICB) therapy. Nevertheless, about half of MMRd tumors do not respond to ICB for unclear reasons. While tumor cell line transplant models of MMRd have reinforced the importance of TMB in immune response, critical questions remain regarding the role of immunosurveillance in the evolution of MMRd tumors induced in vivo. Here, we developed autochthonous mouse models of lung and colon cancer with highly efficient ablation of MMR genes via in vivo CRISPR/Cas9 targeting. Surprisingly, MMRd in these models did not result in increased immunogenicity or response to ICB. Mechanistically, we showed this lack of immunogenicity to be driven by profound intratumoral heterogeneity (ITH). Studies in animals depleted of T cells further demonstrated that immunosurveillance in MMRd tumors has no impact on TMB but shapes the clonal architecture of neoantigens by exacerbating ITH. These results provide important context for understanding immune evasion in cancers with high TMB and have major implications for therapies aimed at increasing TMB.
Feedforward regulatory logic underlies robustness of the specification-to-differentiation transition and fidelity of terminal cell fate duringC. elegansendoderm development
Authors: Ewe Chee Kiang , Sommermann Erica M. , Kenchel Josh , Flowers Sagen E. , Maduro Morris F. , Rothman Joel H.
Published: August 2021

Development is driven by gene regulatory networks (GRNs) that progressively dictate specification and differentiation of cell fates. The architecture of GRNs directly determines the specificity and accuracy of developmental outcomes. We report here that the core regulatory circuitry for endoderm development inC. elegansis comprised of a recursive series of interlocked feedforward modules linking a cascade of six sequentially expressed GATA-type transcription factors. This structure results in a reiterated sequential redundancy, in which removal of a single factor or alternate factors in the cascade results in no, or a mild, effect on endoderm development and gut differentiation, while elimination of any two factors that are sequentially deployed in the cascade invariably results in a strong phenotype. The strength of the observed phenotypes is successfully predicted by a computational model based on the timing and levels of transcriptional states. The feedforward regulatory logic in the GRN appears to ensure timely onset of terminal differentiation genes and allows rapid and robust lockdown of cell fate during early embryogenesis. We further found that specification-to-differentiation transition is linked through a common regulator, the END-1 GATA factor that straddles the two processes. Finally, we revealed roles for key GATA factors in establishing spatial regulatory state domains by acting as transcriptional repressors that appear to define the boundaries of the digestive tract. Our findings support a comprehensive model of the core gene network that describes how robust endoderm development is achieved duringC. elegansembryogenesis.

Graphic abstract
ICOS expression is required for maintenance but not the formation of germinal centers in the spleen in response to P. yoelii infection
Authors: O’Neal Kara A. , Latham Leah E. , Ntirandekura Enatha , Foscue Camille L. , Stumhofer Jason S.
Published: August 2021

Inducible T cell co-stimulator (ICOS) plays a key role in the differentiation and maintenance of follicular helper T (Tfh) cells and thus germinal center (GC) formation. Previously, our lab showed in a Plasmodium chabaudi infection model that Icos-/- mice did not form GCs despite a persistent infection and thus a continued antigen (Ag) load. Here, we show that resolution of a primary infection with P. yoelii, was delayed in Icos-/- mice. This phenotype was associated with a reduction in the accumulation of Tfh-like and GC Tfh cells and an early deficiency in Ag-specific antibody (Ab) production. However, Icos-/- mice maintained their ability to form GCs, though they were less frequent in number than in wild-type (WT) mice. Furthermore, while Ab production in Icos-/- mice matched that of WT mice after the infection cleared, the Abs lacked signs of affinity maturation, suggesting functional defects associated with these GCs. Eventually, these GC structures dissipated more rapidly in Icos-/- mice than in WT mice. Moreover, the ability of Icos-/- mice to form these GC structures is not reliant on the high Ag load associated with P. yoelii infections, as GC formation was preserved in Icos-/- mice treated with early with atovaquone. Finally, mice were unable to form secondary GCs in the absence of ICOS after re-challenge. Overall, these data demonstrate the necessity of ICOS in the maintenance of Tfh cells, the formation and maintenance of sufficient numbers of functioning GCs, and the ability to generate new GC structures after re-infection with P. yoelii.
The cyclin Cln1 controls polyploid titan cell formation following a stress-induced G2 arrest in Cryptococcus
Authors: Altamirano Sophie , Li Zhongming , Fu Man Shun , Ding Minna , Fulton Sophie R. , Yoder J. Marina , Tran Vy , Nielsen Kirsten
Published: August 2021

The pathogenic yeast Cryptococcus neoformans produces polyploid titan cells in response to the host lung environment that are critical for host adaptation and subsequent disease. We analyzed the in vivo and in vitro cell cycles to identify key aspects of the C. neoformans cell cycle that are important for the formation of titan cells. We identified unbudded 2C cells, referred to as a G2 arrest, produced both in vivo and in vitro in response to various stresses. Deletion of the non-essential cyclin Cln1 resulted in over-production of titan cells in vivo, and transient morphology defects upon release from stationary phase in vivo. Using a copper-repressible promoter PCTR4-CLN1 strain and a two-step in vitro titan cell formation assay, our in vitro studies revealed Cln1 functions after the G2 arrest. These studies highlight unique cell cycle alterations in C. neoformans that ultimately promote genomic diversity and virulence in this important fungal pathogen.

Importance

Dysregulation of the cell cycle underlies many human genetic diseases and cancers. Yet numerous organisms, including microbes, also manipulate the cell cycle to generate both morphologic and genetic diversity as a natural mechanism to enhance their chances for survival. The eukaryotic pathogen Cryptococcus neoformans generates morphologically distinct polyploid titan cells critical for host adaptation and subsequent disease. We analyzed the C. neoformans in vivo and in vitro cell cycles to identify changes required to generate the polyploid titan cells. C. neoformans paused cell cycle progression in response to various environmental stresses after DNA replication and before morphological changes associated with cell division, referred to as a G2 arrest. Release from this G2 arrest was coordinated by the cyclin Cln1. Reduced CLN1 expression after the G2 arrest was associated with polyploid titan cell production. These results demonstrate a mechanism to generate genomic diversity in eukaryotic cells through manipulation of the cell cycle that has broad disease implications.
Characterization of a novel Lbx1 mouse loss of function strain
Authors: Decourtye Lyvianne , McCallum-Loudeac Jeremy A. , Zellhuber-McMillan Sylvia , Young Emma , Sircombe Kathleen J. , Wilson Megan J.
Published: August 2021

Adolescent Idiopathic Scoliosis (AIS) is the most common type of spine deformity affecting 2-3% of the population worldwide. The etiology of this disease is still poorly understood. Several GWAS studies have identified single nucleotide polymorphisms (SNPs) located near the gene LBX1 that is significantly correlated with AIS risk. LBX1 is a transcription factor with roles in myocyte precursor migration, cardiac neural crest specification, and neuronal fate determination in the neural tube. Here, we further investigated the role of LBX1 in the developing spinal cord of mouse embryos using a CRISPR-generated mouse model expressing a truncated version of LBX1 (Lbx1Δ). Homozygous mice died at birth, likely due to cardiac abnormalities. To further study the neural tube phenotype, we used RNA-sequencing to identify 410 genes differentially expressed between the neural tubes of E12.5 wildtype and Lbx1Δ/Δ embryos. Genes with increased expression in the deletion line were involved in neurogenesis and those with broad roles in embryonic development. Many of these genes have also been associated with scoliotic phenotypes. In comparison, genes with decreased expression were primarily involved in skeletal development. Subsequent skeletal and immunohistochemistry analysis further confirmed these results. This study aids in understanding the significance of links between Lbx1 function and AIS susceptibility.
Neutralization of the anthrax toxin by antibody-mediated stapling of its membrane-penetrating loop
Authors: Hoelzgen F. , Zalk R. , Alcalay R. , Cohen-Schwartz S. , Garau G. , Shahar A. , Mazor O. , Frank G. A.
Published: August 2021

Anthrax infection is associated with severe illness and high mortality. Protective antigen (PA) is the central component of the anthrax toxin, which is one of two major virulence factors of Bacillus anthracis, the causative agent of anthrax disease. Upon endocytosis, PA opens a pore in the membranes of endosomes, through which the cytotoxic enzymes of the toxin are extruded. The PA pore is formed by a cooperative conformational change in which the membrane-penetrating loops of PA associate, forming a hydrophobic rim that pierces the membrane. Due to its crucial role in anthrax progression, PA is an important target for monoclonal antibody-based therapy. cAb29 is a highly effective neutralizing antibody against PA. Here, the cryo-EM structure of PA in complex with the Fab portion of cAb29 was determined. It was found that cAb29 neutralizes the toxin by clamping the membrane-penetrating loop of PA to the static surface-exposed loop of the D3 domain of the same subunit, thereby preventing pore formation. These results provide the structural basis for the antibody-based neutralization of PA and bring into focus the membrane-penetrating loop of PA as a target for the development of better anti-anthrax vaccines.
Comparison of biopolymer-based edible coatings incorporating Piper nigrum and Schinus terebinthifolia applied on minimally processed pineapple
Authors: de Araujo Camila Ianhes Martins , Bonato Leticia Bicudo , Mangucci Carolina Bragine , Malpass Geoffroy Roger Pointer , Okura Mônica Hitomi , Granato Ana Claudia
Published: August 2021

Purpose

The purpose of this study was to prepare alginate and chitosan-based edible coatings incorporating Schinus terebinthifolia and Piper nigrum essential oils. The prepared films were applied on minimally processed pineapple to study the microbial inhibition of Gram + and Gram – bacteria and fungi and to evaluate the shelf life of the minimally processed fruit.

Design/methodology/approach

In this study alginate and chitosan-based edible coating were prepared and applied on minimally processed pineapple. The edible coatings were evaluated microscopically, by the power of reducing microbial contamination, by the shelf-life improvement.

Findings

This study demonstrates that the incorporation of the essential oils P. nigrum and S. terebinthifolia contributed to the inhibition of all the microorganisms studied and improved the shelf life of minimally processed pineapple. This is especially true for P. nigrum in the chitosan-based edible coating, where the shelf life was improved by 45 days.

Research limitations/implications

Because of the pandemic, it was not possible to perform the sensory analyses of the antimicrobial alginate and chitosan-based edible coatings prepared.

Practical implications

From the results obtained, it is possible to state that the antimicrobial alginate and chitosan-based edible coatings incorporating S. terebinthifolia and P. nigrum essential oils can be used on minimally processed fruits and prolong their shelf life.

Social implications

Due to the lifestyle of modern consumers, who demand speed and practicality and the need to consume fruits for health and quality of life, minimally processed fruits covered with edible coatings incorporating natural antimicrobial additives can provide a practical solution.

Originality/value

To the best of the authors’ knowledge, this is the first time that alginate and chitosan-based edible coatings that incorporate P. nigrum and S. terebinthifolia applied on minimally processed fruit, have been studied.