bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of science journalism reveals gender and regional disparities in coverage
Authors: Davidson Natalie R. , Greene Casey S.
Published: June 2021

Science journalism is a critical way for the public to learn about and benefit from scientific findings. Such journalism shapes the public’s view of the current state of science and legitimizes experts. Journalists can only cite and quote a limited number of sources, who they may discover in their research, including recommendations by other scientists. Biases in either process may influence who is identified and ultimately included as a source. To examine potential biases in science journalism, we analyzed 22,001 non-research articles published by Nature and compared these with Nature-published research articles with respect to predicted gender and name origin. We extracted cited authors’ names and those of quoted speakers. While citations and quotations within a piece do not reflect the entire information-gathering process, they can provide insight into the demographics of visible sources. We then predicted gender and name origin of the cited authors and speakers. We compared articles with a comparator set made up of first and last authors within primary research articles in Nature and a subset of Springer Nature articles in the same time period. In our analysis, we found a skew toward quoting men in Nature science journalism. However, quotation is trending toward equal representation at a faster rate than authorship rates in academic publishing. Gender disparity in Nature quotes was dependent on the article type. We found a significant over-representation of names with predicted Celtic/English origin and under-representation of names with a predicted East Asian origin in both in extracted quotes and journal citations but dampened in citations.
Gene editing in bacteria via SpCas9/sgRNA ribonucleoprotein complexes
Authors: Arroyo-Olarte Rubén Dario , Bravo Rodríguez Ricardo , Morales-Ríos Edgar
Published: June 2021

Gene editing has been revolutionized by CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas technology in a variety of organisms. In bacteria, however, CRISPR-Cas still holds many caveats such as high toxicity of Cas9 and off-target editing effects. In this work we develop a system for the incorporation of Cas9/single guide RNA ribonucleoprotein complexes in bacteria and their successful application for gene editing via homologous recombination. Targeting of a green fluorescent protein (GFP) reporter allows for easy verification of gene-edition via conversion to blue-fluorescent protein (BFP), mediated by the well characterized 196T > C (Tyr66His) mutation.
Timing of transcriptomic peripheral blood mononuclear cell responses of sheep to Fasciola hepatica infection differs from those of cattle, reflecting different disease phenotypes
Authors: Niedziela Dagmara A. , Naranjo-Lucena Amalia , Molina-Hernández Verónica , Browne John A. , Martínez-Moreno Álvaro , Pérez José , MacHugh David E. , Mulcahy Grace
Published: June 2021

Infection with the zoonotic trematode Fasciola hepatica, common in many regions with a temperate climate, leads to delayed growth and loss of productivity in cattle, while infection in sheep can have more severe effects, potentially leading to death. Previous transcriptomic analyses revealed upregulation of TGFB1, cell death and Toll-like receptor signalling, T-cell activation, and inhibition of nitric oxide production in macrophages in response to infection. However, the differences between ovine and bovine responses have not yet been explored. The objective of this study was to further investigate the transcriptomic response of ovine peripheral blood mononuclear cells (PBMC) to F. hepatica infection, and to elucidate the differences between ovine and bovine PBMC responses.

Sixteen male Merino sheep were randomly assigned to infected or control groups (n = 8 per group) and orally infected with 120 F. hepatica metacercariae. Transcriptomic data was generated from PBMC at 0, 2 and 16 weeks post-infection (wpi), and analysed for differentially expressed (DE) genes between infected and control animals at each time point (analysis 1), and for each group relative to time 0 (analysis 2). Analysis 2 was then compared to a similar study performed previously on bovine PBMC.

A total of 453 DE genes were found at 2 wpi, and 2 DE genes at 16 wpi (FDR < 0.1, analysis 1). Significantly overrepresented biological pathways at 2 wpi included role of PKR in interferon induction and anti-viral response, death receptor signalling and RIG-I-like receptor signalling, which suggested that an activation of innate response to intracellular nucleic acids and inhibition of cellular apoptosis were taking place. Comparison of analysis 2 with the previous bovine transcriptomic study revealed that anti-inflammatory response pathways which were significantly overrepresented in the acute phase in cattle, including IL-10 signalling, Th2 pathway, and Th1 and Th2 activation were upregulated only in the chronic phase in sheep. We propose that the earlier activation of anti-inflammatory responses in cattle, as compared with sheep, may be related to the general absence of acute clinical signs in cattle. These findings offer scope for “smart vaccination” strategies for this important livestock parasite.
Mapping the invisible chromatin transactions of prophase chromosome remodelling
Authors: Samejima Itaru , Spanos Christos , Samejima Kumiko , Rappsilber Juri , Kustatscher Georg , Earnshaw William C.
Published: June 2021

We have used a combination of chemical genetics, chromatin proteomics and imaging to map the earliest chromatin transactions during vertebrate cell entry into mitosis. Chicken DT40 CDK1ascells undergo synchronous mitotic entry within 15 minutes following release from a 1NM-PP1-induced arrest in late G2. In addition to changes in chromatin association with nuclear pores and the nuclear envelope, earliest prophase is dominated by changes in the association of ribonucleoproteins with chromatin, particularly in the nucleolus, where pre-rRNA processing factors leave chromatin significantly before RNA polymerase I. Nuclear envelope barrier function is lost early in prophase and cytoplasmic proteins begin to accumulate on the chromatin. As a result, outer kinetochore assembly appears complete by nuclear envelope breakdown (NEBD). Most interphase chromatin proteins remain associated with chromatin until NEBD, after which their levels drop sharply. An interactive proteomic map of chromatin transactions during mitotic entry is available as a resource athttps://mitoChEP.bio.ed.ac.uk.
Langevin dynamics simulation of protein dynamics in nanopores at microsecond timescales
Authors: Mahalik J. P. , Cifello Jeffrey , Muthukumar Murugappan
Published: June 2021

With rapid advancement in the fields of nanopore analysis of protein, it has become imperative to develop modeling framework for understanding the protein dynamics in nanopores. Such modeling framework should include the effects of electro-osmosis, as it plays significant role during protein translocation in confinement. Currently, the molecular dynamics simulations that include the hydrodynamic effects are limited to a timescale of few 100 ns. These simulations give insight about important events like protein unfolding which occurs in this timescale. But many electrophoresis experiments are limited by a detector resolution of ~ 2.5 μs. Analytical theory has been used to interpret protein dynamics at such large timescale. There is a need for molecular modeling of more complex environment and protein shapes which cannot be accounted for by analytical theory. We have developed a framework to study globular protein dynamics in nanopores by using langevin dynamics on a rigid body model of protein and the hydrodynamics is accounted by analytical theory for simple cylindrical nanopore geometry. This framework has been applied to study the dynamics of Ubiquitin translocation in SiNx nanopore by Nir et al26. They have reported 7 times decrease in average dwell time of the protein inside the nanopore in response to a small change in pH from 7.0 to 7.2 and the modification of protein charge was attributed for such drastic change. Closer examination using our simulation revealed that the electro-osmotic effects originating due to very small change in the surface electrostatic potential of the nanopore could lead to such a drastic change in protein dynamics.
Chronic temperature stress effects on the liver proteome of two threespine stickleback (Gasterosteus aculeatus) populations using a novel DIA assay library
Authors: Levitan Bryn Bo , Kültz Dietmar
Published: June 2021

A data-independent acquisition (DIA) assay library was generated for the liver of threespine sticklebacks to evaluate alterations in protein abundance and functional enrichment of molecular pathways following either chronic warm (25°C) or cold (7°C) three-week temperature challenge in two estuarine populations. The DIA assay library was created from a data-dependent acquisition (DDA) based raw spectral library that was filtered to remove low quality or ambiguous peptides. Functional enrichment analyses using STRING identified larger networks that were significantly enriched by examining both the entire liver proteome and only significantly elevated or depleted proteins from the various comparisons. These systems level analyses revealed the unique liver proteomic signatures of two populations of threespine sticklebacks acclimated to chronic temperature stress. The Big lagoon population (BL) had a stronger response than the Klamath river population (KL). At 7°C, BL showed alterations in protein homeostasis that likely fueled a higher demand for energy, but both populations successfully acclimated to this temperature. The warm acclimation induced major increases in proteins involved in chromatin structure and transcription, while there were decreases in proteins related to translation and fatty acid metabolism. Functional enrichment analyses of the entire liver proteome uncovered differences in glycolysis and carbohydrate metabolism between the two populations and between the cold acclimated and control groups. We conclude that the synchronous regulatory patterns of many proteins observed in the liver of threespine sticklebacks provide more comprehensive insight into population-specific responses to thermal stress than the use of less specific pre-determined biomarkers.
Immunosuppressive traits of the hybrid epithelial/mesenchymal phenotype
Authors: Sahoo Sarthak , Nayak Sonali Priyadarshini , Hari Kishore , Purkait Prithu , Mandal Susmita , Kishore Akash , Levine Herbert , Jolly Mohit Kumar
Published: June 2021

Recent preclinical and clinical data suggests enhanced metastatic fitness of hybrid epithelial/ mesenchymal (E/M) phenotypes, but mechanistic details regarding their survival strategies during metastasis remain unclear. Here, we investigate immune-evasive strategies of hybrid E/M states. We construct and simulate the dynamics of a minimalistic regulatory network encompassing the known associations among regulators of EMT (epithelial-mesenchymal transition) and PD-L1, an established immune-suppressor. Our model simulations, integrated with single-cell and bulk RNA-seq data analysis, elucidate that hybrid E/M cells can have high levels of PD-L1, similar to those seen in cells with a full EMT phenotype, thus obviating the need for cancer cells to undergo a full EMT to be immune-evasive. Specifically, in breast cancer, we show the co-existence of hybrid E/M phenotypes, enhanced resistance to anti-estrogen therapy and increased PD-L1 levels. Our results underscore how the emergent dynamics of interconnected regulatory networks can coordinate different axes of cellular fitness during metastasis.
Coupled dynamics of charged macromolecules and counterions mediated by binding enzymes
Authors: Singha Tapas , Li Siao-Fong , Muthukumar Murugappan
Published: June 2021

We investigate the role of active coupling on the transport properties of the macromolecules. The active coupling comes due to bound enzymes with a segment of the macromolecule wherein the enzyme exerts an electrostatic force on the segment of the macromolecule, and eventually, it gets unbound due to the thermal fluctuations. This binding and unbinding process generates active fluctuations in the dynamics of the macromolecule. Starting with segment dynamics and correlations for three dynamical models with active coupling, we obtain the cooperative diffusivity for the realistic charged macromolecules with hydrodynamics. First, we construct the three models by incorporating the features of a real polymer systematically, starting from simple Rouse dynamics with active coupling. We further include segment-segment interactions and in addition, hydrodynamic interactions with active coupling. Our obtained scaling form for segment-segment correlations for the models in terms of the size exponent of the polymer indicating that hydrodynamic and segment-segment interactions along with the active coupling lead to new scaling regimes. We finally study the dynamics of a homogeneously charged flexible polymer in an infinitely dilute solution where enzymes and counterions affect the dynamics of the polymers. We analytically investigate how these active fluctuations affect the coupled dynamics of the polymer and counterions. It turns out that these active fluctuations enhance the effective diffusivity of the polymer. The derived closed-form expression for diffusivity is pertinent to accurate interpretation of light scattering data on multi-component systems with binding-unbinding equilibria.
An artificial host system enables the obligate parasitic plant Cuscuta campestris to grow and complete its life cycle in vitro
Authors: Bernal-Galeano Vivian , Westwood James H.
Published: June 2021

Cuscuta campestris is an obligate parasitic plant that requires a host to complete its lifecycle. Parasite-host connections occur via an haustorium, a unique organ that acts as a bridge for the uptake of water, nutrients and macromolecules. Research on Cuscuta is often complicated by host influences, but comparable systems for growing the parasite in the absence of a host do not exist. We developed an axenic method to grow C. campestris on an Artificial Host System (AHS). We evaluated the effects of nutrients and phytohormones on parasite haustoria development and growth. Haustorium morphology and gene expression were characterized. The AHS consists of an inert, fibrous stick that mimics a host stem, wicking water and nutrients to the parasite. It enables C. campestris to exhibit a parasitic habit and develop through all stages of its lifecycle, including production of new shoots and viable seeds. Phytohormones NAA and BA affect haustoria morphology, and increase parasite fresh weight and biomass. Gene expression in AHS haustoria reflect process similar to those in haustoria on actual host plants. The AHS is a methodological improvement for studying Cuscuta biology by avoiding specific host effects on parasite and giving researchers full control of the parasite environment.
Voltage-driven polyelectrolyte complexation inside a nanopore
Authors: Tripathi Prabhat , Jeon Byoung-jin , Muthukumar Murugappan
Published: June 2021

We have investigated how a pair of oppositely charged macromolecules can be driven by an electric field to form a polyelectrolyte complex inside a nanopore. To observe and isolate an individual complex pair, a model protein nanopore, embedded in artificial phospholipid membrane, allowing compartmentalization (cis/trans) is employed. A polyanion in the cis and a polycation in the trans compartments are subjected to electrophoretic capture by the pore. We find that the measured ionic current across the pore has a distinguishable signature of complex formation, which is different from the signature of the passage of individual molecules through the pore. The ionic current signature allows us to detect the interaction between the two oppositely charged macromolecules and thus, enables us to measure the lifetime of the complex inside the nanopore. After showing that we can isolate a complex pair in the nanopore, we studied the effects of molecular identity on the nature of interaction in different complex pairs. In contrast to the irreversible conductance state of the alpha-hemolysin (αHL) channel in the complexation of poly-styrene-sulfonate (PSS) and poly-L-lysine (PLL), a reversible conductance state is observed during complexation between single stranded DNA (ssDNA) and PLL. This suggests that there is a weak interaction between ssDNA and PLL, when compared to the interaction in a PSS–PLL complex. Analysis of the PSS-PLL complexation events and its lifetime inside the nanopore supports a four step-mechanism: (i) The polyanion is captured by the pore, (ii) the polyanion starts threading through the pore. (iii) The polycation is captured, a complex pair is formed in the pore, and the polyanion slides along the polycation. (iv) The complex pair can be pulled through the pore into the trans compartment or it can dissociate. Additionally, we have developed a simple theoretical model, which describes the lifetime of the complex inside the pore. The observed reversible two-state conductance across αHL channel during ssDNA-PLL complexation, is described as the binding/unbinding of PLL during the translocation of ssDNA. This enables us to evaluate the apparent rate constants for association/dissociation and equilibrium dissociation constants for the interaction of PLL with ssDNA. This work throws light on the behavior of polyelectrolyte complexes in an electric field and enhances our understanding of the electrical aspects of inter-macromolecular interactions, which plays an extremely important role in the organization of macromolecules in the crowded and confined cellular environment.
Notch-dependent Abl signaling regulates cell motility during ommatidial rotation in Drosophila
Authors: Koca Yildiz , Vuong Linh T. , Singh Jaskirat , Giniger Edward , Mlodzik Marek
Published: June 2021

A collective cell motility event that occurs during Drosophila eye development, ommatidial rotation (OR), serves as a paradigm for signaling pathway-regulated directed movement of cell clusters. OR is instructed by several signaling events, including the EGFR and Notch pathways, and planar cell polarity (PCP) signaling, all of which are associated with photoreceptor R3 and R4 specification and differentiation. Here, we show that Abl kinase negatively regulates ommatidial rotation through its activity in the R3/R4 pair. Interestingly in wild-type, Abl is localized to apical junctional regions in R4 but not in R3 during OR, and this apical enrichment requires Notch signaling. We further demonstrate that Abl and Notch genetically interact during OR, and Abl co-immunoprecipitates in complexes with Notch in the developing eye disc. Perturbations of Abl interfere with adherens junction dynamics of the ommatidial preclusters, which are critical for the OR process. Taken together, our data suggest a model in which Abl kinase acts directly downstream of the Notch receptor in R4 to fine-tune OR via its input into adherens junction complexes.
ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR
Authors: Sharma Ankush , Akshay Akshay , Rogne Marie , Eskeland Ragnhild
Published: June 2021

Motivation

Mapping of chromatin accessibility landscapes in single-cells and the integration with gene expression enables a better understanding of gene regulatory mechanisms defining cell identities and cell-fate determination in development and disease. Generally, raw data generated from single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) are deposited in repositories that are inaccessible due to lack of in-depth knowledge of computational programming.

Results

We have developed ShinyArchR.UiO, an R-based shiny app, that facilitates scATAC-seq data accessibility and visualisation in a user-friendly, interactive, and open-source web interface. ShinyArchR.UiO is a tool that can streamline collaborative efforts for interpretation of massive chromatin accessible data and promotes open access data sharing for wider audiences.

Availability and implementation

ShinyArchR.UiO is available at https://Github.com/EskelandLab/ShinyArchRUiO and a demo server set up with a haematopoietic tutorial dataset: https://cancell.medisin.uio.no/ShinyArchR.UiO

Contact

Ankush.Sharma@medisin.uio.no & Ragnhild.Eskeland@medisin.uio.no
Modeling the impact of data sharing on variant classification
Authors: Casaletto James , Cline Melissa , Shirts Brian
Published: June 2021

Objective

Many genetic variants are classified, but many more are designated as variants of uncertain significance (VUS). Patient data may provide sufficient evidence to classify VUS. Understanding how long it would take to accumulate sufficient patient data to classify VUS can inform many important decisions such as data sharing, disease management, and functional assay development.

Materials and Methods

Our software models accumulation of clinical data and their impact on variant interpretation to illustrate the time and probability for variants to be classified when clinical laboratories share evidence, when they silo evidence, and when they share only variant interpretations.

Results

Our models show that the probability of classifying a rare pathogenic variant with an allele frequency of 1/100,000 (1e-05) from less than 25% with no data sharing to nearly 80% after one year when labs share data, with nearly 100% classification after 5 years. Conversely, our models found that extremely rare (1/1,000,000 or 1e-06) variants have a low probability of classification using only clinical data.

Discussion

These results quantify the utility of data sharing and demonstrate the importance of alternative lines of evidence for the interpretation of rare variants. Understanding variant classification circumstances and timelines provides valuable insight for data owners, patients, and service providers. While our modeling parameters are based on assumptions of the rate of accumulation of clinical observations, users may experiment with the impact of these rates by downloading the software and rerunning the simulations with updated parameters.

Conclusion

The modeling software is available at https://github.com/BRCAChallenge/classification-timelines.
The green tea catechin EGCG provides proof-of-concept for a pan-coronavirus entry inhibitor
Authors: LeBlanc Emmanuelle V. , Colpitts Che C.
Published: June 2021

The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has emphasized the serious threat to human health posed by emerging coronaviruses. Effective antiviral countermeasures are urgently needed as vaccine development and deployment against an emerging coronavirus takes time, even in the best-case scenario. The green tea catechin, epigallocatechin gallate (EGCG), has broad spectrum antiviral activity. We demonstrate here that EGCG prevents murine and human coronavirus infection and blocks the entry of lentiviral particles pseudotyped with spike proteins from highly pathogenic coronaviruses, as well as a bat coronavirus poised to emerge into humans. We show that EGCG treatment reduces coronavirus attachment to target cell surfaces. Our results demonstrate the potential for the development of pan-coronavirus attachment inhibitors to protect against current and future emerging coronaviruses.
SPIKE-TRIGGERED INTRASPINAL MICROSTIMULATION IMPROVES MOTOR PERFORMANCE IN AN AMBULATORY RAT MODEL OF SPINAL CORD INJURY
Authors: Borrell Jordan A. , Gattozzi Domenico , Krizsan-Agbas Dora , Jaeschke Matthew W. , Nudo Randolph J. , Frost Shawn B.
Published: June 2021

The purpose of this study was to determine if spike-triggered intraspinal microstimulation (ISMS) results in improved motor performance in an ambulatory rat model of spinal cord injury (SCI). Experiments were carried out in adult male Sprague Dawley rats with 175 kdyn moderate T8 contusion injury. Rats were randomly assigned to one of two groups: Control or Activity Dependent Stimulation (ADS) therapy. Four weeks post-SCI, all rats were implanted with a recording electrode in the left hindlimb motor cortex and a fine-wire, custom-made stimulating electrode in the contralateral lumbar spinal cord. Intracortical and intraspinal microstimulation were used to find sites of similar hip representation areas, which were paired together for ADS therapy. In the ADS therapy group, spike-stimulus conditioning was administered for 4 hours/day, 4 days/week, for 4 weeks via a tethered cable in a testing chamber. During therapy sessions, single-unit spikes were discriminated in real time in the hindlimb motor cortex and used to trigger stimulation in the spinal cord ventral horn. The optimal stimulus intensity (50% ISMS movement threshold) and spike-stimulus delay (10ms) determined in preliminary anesthetized preparations were used during ADS. Control rats were similarly implanted with electrodes but did not receive stimulation therapy. Motor performances of each rat were evaluated before SCI contusion, once a week post-SCI for four weeks (prior to electrode implantation), and once a week post-conditioning for four weeks. Behavioral testing included BBB scoring, Ledged Beam walking, Horizontal Ladder walking, treadmill kinematics via the DigiGait and TreadScan system, and open field walking using OptiTrack kinematic analysis. BBB scores were significantly improved in ADS rats compared to Control rats after 1 week of therapy. In the ADS therapy rats, BBB scores were significantly improved after two weeks of ADS therapy when compared to pre-therapy. Foot fault scores on the Horizontal Ladder were significantly lower in ADS rats compared to pre-therapy ADS and Control rats after 1 week of therapy and returned to pre-injury measures after three weeks of ADS therapy. The Ledged Beam test and kinematic analysis using the DigiGait and TreadScan system showed deficits after SCI in both ADS and Control rats but there were no significant differences between groups after 4 weeks of ADS therapy. These results show that activity dependent stimulation after spinal cord injury using spike-triggered ISMS enhances behavioral recovery of locomotor function as measured by the BBB score and the Horizontal Ladder task.
Time-scales modulate optimal lysis-lysogeny decision switches and near-term phage fitness
Authors: Shivam Shashwat , Li Guanlin , Lucia-Sanz Adriana , Weitz Joshua S.
Published: June 2021

Temperate phage can initiate lysis or lysogeny after infecting a bacterial host. The genetic switch between lysis and lysogeny is mediated by phage regulatory genes as well as host and environmental factors. Recently, a new class of decision switches was identified in phage of the SPbeta group, mediated by the extracellular release of small, phage-encoded peptides termed arbitrium. Arbitrium peptides can be taken up by bacteria prior to infection, modulating the decision switch in the event of a subsequent phage infection. Increasing concentration of arbitrium increases the chance that a phage infection will lead to lysogeny, rather than lysis. Although prior work has centered on the molecular mechanisms of arbitrium-induced switching, here we focus on how selective pressures impact the benefits of plasticity in switching responses. In this work, we examine the possible advantages of near-term adaptation of communication-based decision switches used by the SPbeta-like group. We combine a nonlinear population model with a control theoretic approach to evaluate the relationship between a putative phage reaction norm (i.e., the probability of lysogeny as a function of arbitrium) and the near-term time horizon. We show the adaptive potential of communication-based lysis-lysogeny responses and find that optimal switching between lysis to lysogeny increases near-term fitness compared to fixed responses. We further find that plastic responses are robust to the inclusion of cellular-level stochasticity. These findings provide a principled basis to explore the long-term evolution of phage-encoded decision systems mediated by extracellular decision-signaling molecules, and the feedback between phage reaction norms and ecological context.
Fatty acid dysregulation in the anterior cingulate cortex of depressed suicides with a history of child abuse
Authors: Perlman Kelly , Chouinard-Watkins Raphaël , Tanti Arnaud , Cisbani Giulia , Orri Massimiliano , Turecki Gustavo , Bazinet Richard P , Mechawar Naguib
Published: June 2021

Child abuse (CA) strongly increases the lifetime risk of suffering from major depression and predicts an unfavorable course for the illness. Severe CA has been associated with a specific dysregulation of oligodendrocyte function and thinner myelin sheaths in the human anterior cingulate cortex (ACC) white matter. Given that myelin is extremely lipid-rich, it is plausible that these findings may be accompanied by a disruption of the lipid profile that composes the myelin sheath. This is important to explore since the composition of fatty acids (FA) in myelin phospholipids can influence its stability, permeability, and compactness. Therefore, the objective of this study was to quantify and compare FA concentrations in postmortem ACC white matter in the choline glycerophospholipid pool (ChoGpl), a key myelin phospholipid pool, between adult depressed suicides with a history of CA (DS-CA) matched depressed suicides without CA (DS) and healthy non-psychiatric controls (CTRL). Total lipids were extracted according to the Folch method and separated into respective classes using thin-layer chromatography. FA methyl esters from the ChoGpl fraction were quantified using gas chromatography. Our analysis revealed a strong age-related decrease in most FAs, and specific effects of CA in FAs from the arachidonic acid synthesis pathway, which was further validated with RNA-sequencing data. Furthermore, the concentration of most FAs was found to decrease with age. By extending the previous molecular level findings linking CA with altered myelination in the ACC, these results provide further insights regarding white matter alterations associated with early-life adversity.
Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer
Authors: Achinger-Kawecka Joanna , Stirzaker Clare , Portman Neil , Campbell Elyssa , Chia Kee-Ming , Du Qian , Laven-Law Geraldine , Nair Shalima S. , Yong Aliza , Wilkinson Ashleigh , Clifton Samuel , Milioli Heloise H. , Alexandrou Sarah , Caldon C. Elizabeth , Song Jenny , Khoury Amanda , Meyer Braydon , Gee Julia M.W. , Schmitt Anthony , Wong Emily S. , Hickey Theresa E. , Lim Elgene , Clark Susan J.
Published: June 2021

Three-dimensional (3D) epigenome remodelling is an important mechanism of gene deregulation in cancer. However, its potential as a target to overcome therapy resistance remains largely unaddressed.

Here we show that FDA-approved epigenetic therapy Decitabine (5-Aza-mC) suppresses tumour growth in preclinical metastatic ER+ breast tumour xenograft models. Decitabine-induced genome-wide DNA hypomethylation results in large-scale 3D epigenome deregulation, including de-compaction of higher order chromatin structure and loss of topologically associated domain boundary insulation. Significant DNA hypomethylation at ER-enhancer elements was associated with gain in ER binding, creation of ectopic 3D enhancer-promoter interactions and concordant activation of ER-mediated transcription pathways. Importantly long-term withdrawal of epigenetic therapy partially restores methylation at ER-enhancer elements, resulting in loss of ectopic 3D enhancer-promoter interactions and associated gene repression.

Our study illustrates how epigenetic therapy has potential to target ER+ endocrine-resistant breast cancer by DNA methylation-dependent rewiring of 3D chromatin interactions associated with suppression of tumour growth.
Role of mitochondrial genetic interactions in determining adaptation to high altitude in human population around the globe
Authors: Verma Rahul K , Alena Kalyakulina , Mishra Ankit , Ivanchenko Mikhail , Jalan Sarika
Published: June 2021

Physiological and haplogroup studies performed to understand high-altitude adaptation in humans are limited to individual genes and polymorphic sites. Due to stochastic evolutionary forces, the frequency of a polymorphism is affected by changes in the frequency of a near-by polymorphism on the same DNA sample making them connected in terms of evolution. Here, first we provide a method to model these mitochondrial polymorphisms as “co-mutation networks” for three high-altitude populations, Tibetan, Ethiopian and Andean. Then, by transforming these co-mutation networks into weighted and undirected gene-gene interaction (GGI) networks, we were able to identify functionally enriched genetic interactions of CYB and CO3 genes in Tibetan and Andean populations, while NADH dehydrogenase genes in Ethiopian population playing a significant role in high altitude adaptation. These co-mutation based genetic networks provide insights into the role of different set of genes in high-altitude adaptation human sub-populations.
Classical swine fever virus NS5A inhibits NF-κB signaling by targeting NEMO
Authors: Li Jiaying , Yu Haixiao , Jiang Wenjin , Ma Ping , Feng Zezhong , Lu Yang , Tu Changchun , Sun Jinfu
Published: June 2021

The NS5A non-structural protein of classical swine fever virus (CSFV) is a multifunctional protein involved in viral genomic replication, protein translation and regulation of cellular signaling pathways, and assembly of infectious virus particles. Previous report showed that NS5A inhibited nuclear factor kappa B (NF-κB) signaling induced by poly(I:C); however, the mechanism was not elucidated. Here, we report that NS5A interacts with NF-κB essential modulator (NEMO),a regulatory subunit of the IκB kinase (IKK) complex, and that the zinc finger domain of NEMO essential for NEMO ubiquitination and IKK activation is required for the interaction of NEMO with NS5A. Viral infection or NS5A expression by itself reduced the protein level of NEMO. Mechanistic analysis revealed that NS5A mediated proteasomal degradation of NEMO. Ubiquitination assay showed that NS5A induced K27-but not K48-linked polyubiquitination of NEMO. In addition, NS5A blocked k63-linked polyubiquitination of NEMO, thereby inhibiting activation of IKK and NF-κB. These findings indicate that NS5A inhibits NF-κB signaling by mediating proteasomal degradation of NEMO and blocking k63-linked polyubiquitination of NEMO, thereby revealing a novel mechanism by which CSFV inhibits host innate immunity.

Importance

Classical swine fever (CSF) is a economically important swine viral disease leading to hemorrhagic fever and immuno-suppression. In order to successfully infect and replicate in a host cell, viruses have evolved various strategies to antagonize host innate immunity. It is known that CSFV non-structural protein Npro interacts with interferon regulatory factor 3 (IRF3) and mediates its proteasomal degradation, thereby inhibiting the production of type I interferon. However, no other mechanism by which CSFV antagonizes host innate immunity has so far been reported. Here, we show that NS5A inhibits NF-κB signaling by mediating proteasomal degradation of NEMO and by blocking k63-linked polyubiquitination of NEMO, thereby revealing a novel mechanism by which CSFV antagonizes host innate immunity.
Fate transitions in Drosophila neural lineages: a single cell road map to mature neurons.
Authors: Marques Graça S. , Teles-Reis José , Konstantinides Nikolaos , Brito Patrícia H. , Homem Catarina C. F.
Published: June 2021

Neuron specification and maturation are essential for proper central nervous system development. However, the precise mechanisms that govern neuronal maturation remain poorly understood. Here, we use single-cell RNA sequencing, combined with a conditional genetic strategy to analyse neuronal lineages and their new born neurons in the Drosophila larval brain. A focused analysis on the transcriptional alterations that occur right after neuron generation revealed that neuron maturation starts shortly after neuronal birth, with transcription, but no translation, of mature neuronal features such as neurotransmitter (NT) genes. Using NT gene Choline acetyltransferase as an example, we show that the timings of translation initiation are not solely dependent on neuron age but are rather coordinated with the animal developmental stage. This study is the first characterization of the initial phases of neuron maturation, supporting a model where neuron maturation is coordinated with the animal developmental stage through post-transcriptional regulation of terminal effector genes.
Inhibition of N-myristoyltransferase Promotes Naive Pluripotency in Mouse and Human Pluripotent Stem Cells
Authors: Yoshida Junko , Watanabe Hitomi , Yamauchi Kaori , Nishikubo Takumi , Isotani Ayako , Ohtsuka Satoshi , Niwa Hitoshi , Akutsu Hidenori , Umezawa Akihiro , Suemori Hirofumi , Takashima Yasuhiro , Kondoh Gen , Takeda Junji , Horie Kyoji
Published: June 2021

Naive and primed states are distinct states of pluripotency during early embryonic development that can be captured and converted to each other in vitro. To elucidate the regulatory mechanism of pluripotency, we performed a recessive genetic screen of homozygous mutant mouse embryonic stem cells (mESCs) and found that suppression of N-myristoyltransferase (Nmt) promotes naive pluripotency. Disruption of Nmt1 in mESCs conferred resistance to differentiation. Suppression of Nmt in mouse epiblast stem cells (mEpiSCs) promoted the conversion from the primed to the naive state. This effect was independent of Src, which is a major substrate of Nmt and is known to promote differentiation of mESCs. Suppression of Nmt in naive-state human induced pluripotent stem cells (hiPSCs) increased the expression of the naive-state marker. These results indicate that Nmt is a novel target for the regulation of naive pluripotency conserved between mice and humans.
Contamination detection and microbiome exploration with GRIMER
Authors: Piro Vitor C. , Renard Bernhard Y.
Published: June 2021

Background

Contamination detection is a important step that should be carefully considered in early stages when designing and performing microbiome studies to avoid biased outcomes. Detecting and removing true contaminants is challenging, especially in low-biomass samples or in studies lacking proper controls. Interactive visualizations and analysis platforms are crucial to better guide this step, to help to identify and detect noisy patterns that could potentially be contamination. Additionally, external evidence, like aggregation of several contamination detection methods and the use of common contaminants reported in the literature could help to discover and mitigate contamination.

Results

We propose GRIMER, a tool that performs automated analyses and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata. It unifies several sources of evidence to help detect contamination. GRIMER is independent of quantification methods and directly analyses contingency tables to create an interactive and offline report. Reports can be created in seconds and are accessible for non-specialists, providing an intuitive set of charts to explore data distribution among observations and samples and its connections with external sources. Further, we compiled and used an extensive list of possible external contaminant taxa and common contaminants with 210 genera and 627 species reported in 22 published articles.

Conclusion

GRIMER enables visual data exploration and analysis, supporting contamination detection in microbiome studies. The tool and data presented are open-source and available at:https://gitlab.com/dacs-hpi/grimer.
Quantifying invasibility
Authors: Pande Jayant , Tsubery Yehonatan , Shnerb Nadav M.
Published: June 2021

Invasibility, the chance of a population to grow from rarity and to establish a large-abundance colony, plays a fundamental role in population genetics, ecology, and evolution. For many decades, the mean growth rate when rare has been employed as an invasion criterion. Recent analyses have shown that this criterion fails as a quantitative metric for invasibility, with its magnitude sometimes even increasing while the invasibility decreases. Here we employ a new large-deviations (Wentzel-Kramers-Brillouin, WKB) approach and derive a novel and easy-to-use formula for the chance of invasion in terms of the mean growth rate and its variance. We also explain how to extract the required parameters from abundance time series. The efficacy of the formula, including its accompanying data analysis technique, is demonstrated using synthetic and empirically-calibrated time series from a few canonical models.
Reproductive skew, fitness costs, and winner-loser effects in social-dominance evolution
Authors: Leimar Olof , Bshary Redouan
Published: June 2021

Social hierarchies can increase reproductive skew in group-living animals. Using game theory we investigate how the opportunity for differently ranked individuals to acquire resources influences reproductive skew, costs of hierarchy formation, and winner and loser effects. Individuals adjust their aggressive and submissive behaviour through reinforcement learning. The learning is based on perceived rewards and penalties, which depend on relative fighting ability. From individualbased simulations we determine evolutionary equilibria of traits that control an individual’s learning. We examine situations that differ in the extent of monopolisation of contested resources by dominants and in the amounts of uncontested resources that are distributed independently of rank. With costly fighting, we find that stable dominance hierarchies form, such that reproductive skew mirrors the distribution of resources over ranks. Individuals pay substantial costs of interacting, in particular in high-skew situations, with the highest costs paid by intermediately ranked individuals. For cases where dominants monopolise contested resources there are notable winner and loser effects, with winner effects for high ranks and very pronounced loser effects for lower ranks. The effects are instead weak when acquired resources increase linearly with rank. We compare our results on contest costs and winner-loser effects with field and experimental observations.
Comparison of undirected frequency-domain connectivity measures for cerebro-peripheral analysis
Authors: Gross Joachim , Kluger Daniel S. , Abbasi Omid , Chalas Nikolas , Steingräber Nadine , Daube Christoph , Schoffelen Jan-Mathijs
Published: June 2021

Analyses of cerebro-peripheral connectivity aim to quantify ongoing coupling between brain activity (measured by MEG/EEG) and peripheral signals such as muscle activity, continuous speech, or physiological rhythms (such as pupil dilation or respiration). Due to the distinct rhythmicity of these signals, undirected connectivity is typically assessed in the frequency domain. This leaves the investigator with two critical choices, namely a) the appropriate measure for spectral estimation (i.e., the transformation into the frequency domain) and b) the actual connectivity measure. As there is no consensus regarding best practice, a wide variety of methods has been applied. Here we systematically compare combinations of six standard spectral estimation methods (comprising fast Fourier and continuous wavelet transformation, bandpass filtering, and short-time Fourier transformation) and six connectivity measures (phase-locking value, Gaussian-Copula mutual information, Rayleigh test, weighted pairwise phase consistency, magnitude squared coherence, and entropy). We provide performance measures of each combination for simulated data (with precise control over true connectivity), a single-subject set of real MEG data, and a full group analysis of real MEG data. Our results show that, overall, wppc and gcmi tend to outperform other connectivity measures, while entropy was the only measure sensitive to bimodal deviations from a uniform phase distribution. For group analysis, choosing the appropriate spectral estimation method appeared to be more critical than the connectivity measure. We discuss practical implications (sampling rate, SNR, computation time, and data length) and aim to provide recommendations tailored to particular research questions.
Oleate metabolism using kinetic 13C dilution strategy deciphered the potential role of global transcription regulator arcA in Escherichia coli
Authors: Jindal Shikha , Jyoti Poonam , Venkatesh K.V. , Masakapalli Shyam Kumar
Published: June 2021

Microbial metabolism of long-chain fatty acids (LCFA; > C12) is of relevance owing to their presence in various nutrient niches. Microbes have evolved to metabolize LCFA by expressing relevant genes coordinated by various transcriptional regulators. Among the global transcriptional regulators, the metabolic control conferred by arcA (aerobic respiration control) under a LCFA medium is lacking. This work is targeted to unravel the metabolic features of E.coli MG1655 and its knockout strain ΔarcA under oleate (C18:1) as a sole carbon source, providing novel insights into the flexibility of the global regulators in maintaining the cellular physiology. Owing to the availability and cost of stable isotope LCFA tracers, we adopted a novel kinetic 13C dilution strategy. This allowed us to quantify the 13C dilution rates in the amino acids that retro-biosynthetically shed light on the central metabolic pathways in actively growing cells. Our data comprehensively mapped oleate oxidization in E.coli via the pathways of β-oxidation, TCA cycle, anaplerotic and gluconeogenesis. Interestingly, arcA knockout showed expeditious growth (~60%) along with an increased oleate utilization rate (~55%) relative to the wild-type. ΔarcA also exhibited higher 13C dilution rates (> 20%) in proteinogenic amino acids than the wild-type. Overall, the study established the de-repression effect conferred by ΔarcA in E.coli, which resulted in a phenotype with reprogrammed metabolism favouring higher oleate assimilation. The outcomes suggest rational metabolic engineering of regulators as a strategy to develop smart cells for enhanced biotransformation of LCFA. This study also opens an avenue for adopting a kinetic 13C dilution strategy to decipher the cellular metabolism of a plethora of substrates, including other LCFA in microbes.
Lymphatics regulation of the inflammatory clotting creates the natural on-off switch for the immune ignorance that allows subcutaneous allografting
Authors: Wachowska Małgorzata , Kilarski Witold W
Published: June 2021

The ability of lymph to clot indicates that, like blood vessels, lymphatics must have means to counteract this process. Here, we analyzed lymphatic hemostatic properties, tailoring them for potential therapeutic applications. Inflammatory stimuli induced tissue factor-dependent focal lymph clotting while blocking thrombomodulin leading to widespread but transient occlusion of collecting vessels. Decellularization of lymphatics resulted in tissue factor-independent lymphatic occlusion by widespread and persistent lymph clots. In occluded decellularized ‘ghost’ vessels, fibrin was eventually reperfused. During the regeneration, ghost lymphatics were filled with granuloma-like clusters of antigen-presenting cells and T cells. Despite that, immune response against allografts placed under non-drained skin did not develop as long lymphatics remained occluded, the effect that could be prolonged by delaying regeneration of the decellularized collectors. When the lymph clotting was blocked, decellularized lymphatics could still drain macromolecules and leukocytes, showing that lymphatic endothelium is not necessary for the classic lymphatic functions. The control of excessive clotting emerges as the essential function of lymphatics that could explain the seeming spandrel presence of lymphatic networks in organs such as the kidney or heart, contribute to microvascular thrombosis during infection, and can be exploited to induce immune ignorance of the subcutaneous endocrine grafts.