bluuebunny/crossref_metadata_2025 huggingface dataset:
A CRISPRi screen of essential genes reveals that proteasome regulation dictates acetic acid tolerance inSaccharomyces cerevisiae
Authors: Mukherjee Vaskar , Lind Ulrika , St. Onge Robert P. , Blomberg Anders , Nygård Yvonne
Published: April 2021

CRISPR interference (CRISPRi) is a powerful tool to study cellular physiology under different growth conditions and this technology provides a means for screening changed expression of essential genes. In this study, aSaccharomyces cerevisiaeCRISPRi library was screened for growth in medium supplemented with acetic acid. Acetic acid is a growth inhibitor challenging the use of yeast for industrial conversion of lignocellulosic biomasses. Tolerance towards acetic acid that is released during biomass hydrolysis is crucial for cell factories to be used in biorefineries.

The CRISPRi library screened consists of >9,000 strains, where >98% of all essential and respiratory growth-essential genes were targeted with multiple gRNAs. The screen was performed using the high-throughput, high-resolution Scan-o-matic platform, where each strain is analyzed separately. Our study identified that CRISPRi targeting of genes involved in vesicle formation or organelle transport processes led to severe growth inhibition during acetic acid stress, emphasizing the importance of these intracellular membrane structures in maintaining cell vitality. In contrast, strains in which genes encoding subunits of the 19S regulatory particle of the 26S proteasome were downregulated had increased tolerance to acetic acid, which we hypothesize is due to ATP-salvage through an increased abundance of the 20S core particle that performs ATP-independent protein degradation. This is the first study where a high-resolution CRISPRi library screening paves the way to understand and bioengineer the robustness of yeast against acetic acid stress.

IMPORTANCE

Acetic acid is inhibitory to the growth of the yeastSaccharomyces cerevisiae, causing ATP starvation and oxidative stress, which leads to sub-optimal production of fuels and chemicals from lignocellulosic biomass. In this study, where each strain of a CRISPRi library was characterized individually, many essential and respiratory growth essential genes that regulate tolerance to acetic acid were identified, providing new understanding on the stress response of yeast and new targets for the bioengineering of industrial yeast. Our findings on the fine-tuning of the expression of proteasomal genes leading to increased tolerance to acetic acid suggests that this could be a novel strategy for increasing stress tolerance, leading to improved strains for production of biobased chemicals.
Prevalence of SARS-CoV-2 antibodies in Denmark 2020: results from nationwide, population-based sero-epidemiological surveys
Authors: Espenhain Laura , Tribler Siri , Jørgensen Charlotte Sværke , Holm Hansen Christian , Wolff Sönksen Ute , Ethelberg Steen
Published: April 2021

Background

Seroprevalence studies have proven an important tool to monitor the progression of the coronavirus disease 2019 (COVID-19) epidemic. We present results of consecutive population-based seroprevalence surveys performed in Denmark in 2020.

Methods

Invitation letters including a questionnaire covering symptoms were sent to representatively drawn samples of the population in spring, late summer and autumn/winter of 2020. Blood samples from participants taken at public test-centers were analyzed for total Ig and seroprevalence estimates per population segment calculated and compared to other surveillance parameters.

Results

From 34,081 participating individuals (response rate 33%), we obtained seroprevalence estimates increasing from 1.1% (95%CI: 0.7%–1.7) in May to 4.0 % (95%CI: 3.4%–4.7%) in December 2020. By December 2020, 1.5% of the population 12 years and older had tested positive by PCR. Seroprevalence estimates were roughly 3 times higher in those aged 12-29 compared to 65+ and higher in metropolitan municipalities. Among seropositives, loss of taste/smell were the more specific symptoms, 32%-56% did not report any symptoms. In half of seroconverted families, we did not see evidence of transmission between generations. Infected individuals in older age groups were hospitalized several fold more often than in younger.

Conclusions

Seroprevalence increased during 2020; younger age groups were primarily infected in the autumn/winter surge. Approximately half were asymptomatically infected. Denmark has a high per capita test rate; roughly two undiagnosed infections of COVID-19 were estimated to occur for each diagnosed case. The epidemic appears to have progressed relatively modestly during 2020 in Denmark.

summary

We describe population-based COVID-19 seroprevalence surveys performed in Denmark in 2020. The seroprevalence increased during the year, particularly in adolescents and young adults, but was overall low. Roughly two undiagnosed cases per PCR-confirmed case were detected by December 2020.
PepVAE3: variational autoencoder framework for antimicrobial peptide generation and activity prediction
Authors: Dean Scott N. , Alvarez Jerome Anthony E. , Zabetakis Dan , Walper Scott A. , Malanoski Anthony P.
Published: April 2021

New methods for antimicrobial design are critical for combating pathogenic bacteria in the post-antibiotic era. Fortunately, competition within complex communities has led to the natural evolution of antimicrobial peptide (AMP) sequences that have promising bactericidal properties. Unfortunately, the identification, characterization, and production of AMPs can prove complex and time consuming. Here we report a peptide generation framework, PepVAE3, based around variational autoencoder (VAE) and antimicrobial activity prediction models for designing novel AMPs using only sequences and experimental minimum inhibitory concentration (MIC) data as input. Sampling from distinct regions of the learned latent space allows for controllable generation of new AMP sequences with minimal input parameters. Extensive analysis of the PepVAE3-generated sequences paired with antimicrobial activity prediction models supports this modular design framework as a promising system for development of novel AMPs, demonstrating controlled production of AMPs with experimental validation of predicted antimicrobial activity.
Keratin dynamics govern the establishment of the maternal-fetal interface
Authors: Nahaboo Wallis , Eski Sema Elif , Vermeersch Marjorie , Saykali Bechara , Monteyne Daniel , Magin Thomas M. , Schwarz Nicole , Zwijsen An , Perez-Morga David , Pal Singh Sumeet , Migeotte Isabelle
Published: April 2021

After implantation, the mouse embryo undergoes gastrulation and forms mesoderm and endoderm. Mesoderm participates in embryonic and extra-embryonic tissues including the amnion, yolk sac, chorion and allantois, the umbilical cord precursor.

Extra-embryonic mesoderm is rich in intermediate filaments. Two-photon live imaging of keratin 8-eYFP knock-in embryos allowed recording nucleation and elongation of keratin filaments, which formed apical cables coordinated across multiple cells in amnion, allantois, and blood islands. Embryos lacking all keratins displayed a deflated exocoelomic cavity, a narrow thick amnion, and a short allantois, indicating a hitherto unknown role for keratin filaments in post-implantation extra-embryonic membranes morphogenesis.

Single-cell RNA sequencing of mesoderm cells, microdissected amnion, chorion, and allantois provided an interactive atlas of transcriptomes with germ layer and regional information. Keratin 8highmesenchymal cells in contact with the exocoelom shared a cytoskeleton and adhesion expression profile that might explain the adaptation of extra-embryonic structures to the increasing mechanical pressure.

GRAPHICAL ABSTRACT
Maternal age affects equine Day 8 embryo gene expression both in trophoblast and inner cell mass
Authors: Derisoud E. , Jouneau L. , Dubois C. , Archilla C. , Jaszczyszyn Y. , Legendre R. , Daniel N. , Peynot N. , Dahirel M. , Auclair-Ronzaud J. , Wimel L. , Duranthon V. , Chavatte-Palmer P.
Published: April 2021

Background

Breeding a mare until she is not fertile or even until her death is common in equine industry but the fertility decreases as the mare age increases. Embryo loss due to reduced embryo quality is partly accountable for this observation. Here, the effect of mare’s age on blastocysts’ gene expression was explored. Day 8 post-ovulation embryos were collected from multiparous young (YM, 6-year-old, N = 5) and older (OM, > 10-year-old, N = 6) non-nursing Saddlebred mares, inseminated with the semen of one stallion. Pure or inner cell mass (ICM) enriched trophoblast, obtained by embryo bisection, were RNA sequenced. Deconvolution algorithm was used to discriminate gene expression in the ICM from that in the trophoblast. Differential expression was analyzed with embryo sex and diameter as cofactors. Functional annotation and classification of differentially expressed genes and gene set enrichment analysis were also performed.

Results

Maternal aging did not affect embryo recovery rate, embryo diameter nor total RNA quantity. In both compartments, the expression of genes involved in mitochondria and protein metabolism were disturbed by maternal age, although more genes were affected in the ICM. Mitosis, signaling and adhesion pathways and embryo development were decreased in the ICM of embryos from old mares. In trophoblast, ion movement pathways were affected.

Conclusions

This is the first study showing that maternal age affects gene expression in the equine blastocyst, demonstrating significant effects as early as 10 years of age. These perturbations may affect further embryo development and contribute to decreased fertility due to aging.
The quantitative genetics of the prevalence of infectious diseases: hidden genetic variation due to Indirect Genetic Effects dominates heritable variation and response to selection
Authors: Bijma Piter , Hulst Andries D. , de Jong Mart C. M.
Published: April 2021

Infectious diseases have profound effects on life, both in nature and agriculture. Despite the availability of well-established epidemiological theory, however, a quantitative genetic theory of the host population for the endemic prevalence of infectious diseases is almost entirely lacking. While several studies have demonstrated the relevance of the transmission dynamics of infectious diseases for heritable variation and response to selection of the host population, our current theoretical framework of quantitative genetics excludes these dynamics. As a consequence, we do not know which genetic effects of the host population determine the prevalence of an infection, and have no concepts of breeding value and heritable variation for endemic prevalence.

Here we integrate quantitative genetics and epidemiology, and propose a quantitative genetic theory forR0and for the endemic prevalence of an infectious disease. We first identify the genetic factors that determine the prevalence of an infection, using an approach founded in epidemiological theory. Subsequently we investigate the population level consequences of individual genetic variation, both forR0and for the endemic prevalence. Next, we present expressions for the breeding value and heritable variation, for both prevalence and individual binary disease status, and show that these parameters depend strongly on the level of the prevalence. Results show that heritable variation for endemic prevalence is substantially greater than currently believed, and increases when prevalence approaches zero, while heritability of individual disease status goes to zero. As a consequence, response of prevalence to selection accelerates considerably when prevalence goes down, in contrast to predictions from classical theory. Finally, we show that most of the heritable variation for the endemic prevalence of an infection is hidden due to indirect genetic effects, suggesting a key role for kin-group selection both in the evolutionary history of current populations and for genetic improvement strategies in animals and plants.
Critical re-evaluation of the slope factor of the operational model of agonism: Do not exponentiate operational efficacy
Authors: Jakubík Jan
Published: April 2021

Although being a relative term, agonist efficacy is a cornerstone in the proper assessment of agonist selectivity and signalling bias. The operational model of agonism (OMA) has become successful in the determination of agonist efficacies and ranking them. In 1983, Black and Leff introduced the slope factor to the OMA to make it more flexible and allow for fitting steep as well as flat concentration-response curves. Functional analysis of OMA demonstrates that the slope factor implemented by Black and Leff affects relationships among parameters of the OMA. Fitting of the OMA with Black & Leff slope factor to concentration-response curves theoretical model-based data resulted in wrong estimates of operational efficacy and affinity. In contrast, fitting the OMA modified by the Hill coefficient to the same data resulted in correct estimates of operational efficacy and affinity. Therefore, OMA modified by the Hill coefficient should be preferred over the Black & Leff equation for ranking of agonism and subsequent analysis, like quantification of signalling bias, when concentration-response curves differ in the slope factor and mechanism of action is known. Otherwise. Black & Leff equation should be used with extreme caution acknowledging potential pitfalls.
Genome archaeology of two laboratorySalmonella enterica entericasv Typhimurium
Authors: Zaworski Julie , Dagva Oyut , Kingston Anthony W , Fomenkov Alexey , Morgan Richard D. , Bossi Lionello , Raleigh Elisabeth A.
Published: April 2021

The Salmonella research community has used strains and bacteriophages over decades, exchanging useful new isolates among laboratories for study of cell surface antigens, metabolic pathways and restriction-modification studies. Here we present the sequences of two laboratorySalmonellastrains (STK005, an isolate of LB5000; and its descendant ER3625). In the ancestry of LB5000, segments of ~15 and ~42 kb were introduced fromSalmonella entericasv Abony 103 intoSalmonella entericasv Typhimurium LT2, forming strain SD14; this strain is thus a hybrid ofS. entericaisolates. Strains in the SD14 lineage were used to define flagellar antigens from the 1950s to the 1970s, and to define three restriction-modification systems from the 1960s to the 1980s. LB5000 was also used as host in phage typing systems used by epidemiologists. In the age of cheaper and easier sequencing, this resource will provide access to the sequence that underlies the extensive literature.
Diaphragm muscle fibrosis involves changes in collagen organization with mechanical implications in Duchenne Muscular Dystrophy
Authors: Sahani Ridhi , Wallace C. Hunter , Jones Brian K. , Blemker Silvia S.
Published: April 2021

In Duchenne muscular dystrophy (DMD), diaphragm muscle dysfunction results in respiratory insufficiency, a leading cause of death in patients. Increased muscle stiffness occurs with buildup of fibrotic tissue, characterized by excessive accumulation of extracellular matrix (ECM) components such as collagen. However, changes in mechanical properties are not explained by collagen amount alone and we must consider the complex structure and mechanics of fibrotic tissue. The goals of our study were to (1) determine if and how collagen organization changes with the progression of DMD in diaphragm muscle tissue, and (2) predict how collagen organization influences the mechanical properties of ECM. We first visualized collagen structure with scanning electron microscopy (SEM) images and then developed an analysis framework to quantify collagen organization and generate image-based finite-element models. The image analysis revealed significant age- and disease-dependent increases in collagen fiber straightness and alignment, ranging from 4.7 to 13.4%, but collagen fibers retained a transverse orientation relative to muscle fibers. The mechanical models predicted significant age- and disease-dependent increases in transverse effective stiffness and average stress, ranging from 8.8 to 12.4%. Additionally, both healthy and diseased models revealed an increase in transverse stiffness relative to longitudinal stiffness, with significant age- and disease-dependent increases in the ratio of transverse to longitudinal stiffness, ranging from 19.7 to 24.5%. This study revealed changes in diaphragm ECM structure and mechanics during the progression of disease in themdxmuscular dystrophy mouse phenotype, highlighting the need to consider the role of collagen organization on diaphragm muscle function.
An open source statistical and data processing toolbox for wide-field optical imaging in mice
Authors: Brier Lindsey M. , Culver Joseph P.
Published: April 2021

Wide-field optical imaging (WOI) produces concurrent hemodynamic and cell-specific calcium recordings across the entire cerebral cortex. There have been multiple studies using WOI to image mouse models with various environmental or genetic manipulations to understand various diseases. Despite the obvious utility of pursuing mouse WOI alongside human functional magnetic resonance imaging (fMRI), and the multitude of analysis toolboxes in the fMRI literature, there is not an available open-source, user-friendly data processing and statistical analysis toolbox for WOI data. Here, we present our MATLAB toolbox for pre-processing WOI data, as described and adapted to combine processing techniques from multiple WOI groups. Additionally, we provide multiple data analysis packages and translate two commonly used statistical approaches from the fMRI literature to the WOI data. To illustrate the utility, we demonstrate the ability of the processing and analysis framework to detect a well-established deficit in a mouse model of stroke. Additionally, we evaluate resting state data in healthy mice.
Drought resilience of long term dry-farmed grapevines(Vitis vinifera L.)
Authors: Pagay Vinay , Furlan Tarita S. , Kidman Catherine M. , Nagahatenna Dilrukshi
Published: April 2021

We explored the long-term drought resilience of field-grown unirrigated (or dry-grown) grapevines of pre-clonal origin from shallow (SR) and deep (DR) soils representing low and high soil water availability, respectively, in a warm, Mediterranean climate. Despite lower soil moisture available to SR vines, both deep and shallow-rooted vines had similar vine water status, based on measurements of midday stem water potential (Ψs), and leaf net photosynthesis (An). Due to the lower stomatal conductance (gs), SR had higher intrinsic water use efficiency (WUEi) than DR, however the carbon isotope ratio (δ13C) of the fruit at harvest was similar between the two groups. Our observations suggest a degree of drought adaptation in the SR vines resulting from multi-decadal cyclical droughts. Overall, we demonstrate that pre-clonal Cabernet Sauvignon grapevines dry-grown in shallow soils have an enhanced resilience to drought compared to dry-grown vines in deep soils. This study has implications for selection of crop genetic material in a changing climate.
me31Bregulates stem cell homeostasis by preventing excess dedifferentiation in theDrosophilamale germline
Authors: Jensen Lindy , Venkei Zsolt G. , Watase George J. , Bisai Bitarka , Pletcher Scott , Lee Cheng-Yu , Yamashita Yukiko M.
Published: April 2021

Tissue-specific stem cells maintain tissue homeostasis by providing a continuous supply of differentiated cells throughout the life of organisms. Differentiated/differentiating cells can revert back to a stem cell identity via dedifferentiation to help maintain the stem cell pool beyond the lifetime of individual stem cells. Although dedifferentiation is important to maintain the stem cell population, it is speculated to underlie tumorigenesis. Therefore, this process must be tightly controlled. Here we show that a translational regulatorme31Bplays a critical role in preventing excess dedifferentiation in theDrosophilamale germline: in the absence ofme31B, spermatogonia (SGs) dedifferentiate into germline stem cells (GSCs) at a dramatically elevated frequency. Our results show that the excess dedifferentiation is likely due to misregulation ofnos,a key regulator of germ cell identity and GSC maintenance. Taken together, our data reveal negative regulation of dedifferentiation to balance stem cell maintenance with differentiation.
Human pulmonary artery endothelial cells upregulate ACE2 expression in response to iron-regulatory elements: potential implications for SARS-CoV-2 infection of vascular endothelial cells
Authors: K Toe Quezia , Issitt Theo , S Mahomed Abdul , Panselinas Ioannis , Almaghlouth Fatma , Burke-Gaffney Anne , Wort S John , J Quinlan Gregory
Published: April 2021

Emerging studies from the ongoing covid-19 pandemic have implicated vascular dysfunction and endotheliitis in many patients presenting with severe disease. However, there is limited evidence for the expression of ACE2 (the principal co-receptor for Sars-Cov-2 cellular attachment) in vascular endothelial cells which has prompted the suggestion that the virus does not infect these cell types. However, the studies presented here demonstrate enhanced expression of ACE2 at the level of both mRNA and protein, in human pulmonary artery endothelial cells (PAECs) challenged with either IL-6 or hepcidin. Notably elevated levels both these iron-regulatory elements have been described in Covid-19 patients with severe disease and are further associated with morbidity and mortality. Additionally, levels of both IL-6 and hepcidin are often elevated in the elderly and in chronic disease settings, these populations being at greater risk of adverse outcomes from Sars-Cov-2 infection. A role for IL-6 and hepcidin as modulators of ACE2 expression seems plausible, additional, studies are required to determine if viral infection can be demonstrated in PAECs challenged with either of these iron-regulatory elements.
The role of L-arabinose metabolism forEscherichia coliO157:H7 in edible plants
Authors: Crozier Louise , Marshall Jacqueline , Holmes Ashleigh , Wright Kathryn , Rossez Yannick , Merget Bernhard , Humphries Sonia , Toth Ian , Jackson Robert Wilson , Holden Nicola Jean
Published: April 2021

Arabinose is a major plant aldopentose in the form of arabinans complexed in cell wall polysaccharides or glycoproteins (AGP), but comparatively rare as a monosaccharide. L-arabinose is an important bacterial metabolite, accessed by pectolytic microorganisms such asPectobacterium atrosepticumvia pectin and hemicellulose degrading enzymes. However, not all plant-associated microbes encode cell wall degrading enzymes, yet can metabolise L-arabinose, raising questions about their use of and access to the glycan in plants. Therefore, we examined L-arabinose metabolism in the food-borne pathogenEscherichia coliO157:H7 (isolate Sakai) during its colonisation of plants. L-arabinose metabolism (araBA) and transport (araF) genes were activated at 18 °Cin vitroby L-arabinose and expressed over prolonged periodsin planta. Although deletion ofaraBADdid not impact the colonisation ability ofE. coliO157:H7 (Sakai) on plants,araAwas induced on exposure to spinach cell wall polysaccharides. Furthermore, debranched and arabinan oligosaccharides inducedarametabolism gene expressionin vitro, and stimulated modest proliferation, while immobilised pectin did not. Thus,E. coliO157:H7 (Sakai) can utilise pectin/AGP- derived L-arabinose as a metabolite, but differs fundamentally inaragene organisation, transport and regulation from the related pectinolytic speciesP. atrosepticum, reflective of distinct plant- associated lifestyles.
Emotion Recognition in a Multi-Componential Framework: The Role of Physiology
Authors: Menétrey Maëlan Q. , Mohammadi Gelareh , Leitão Joana , Vuilleumier Patrik
Published: April 2021

Emotions are rich and complex experiences involving various behavioral and physiological responses. While many empirical studies have focused on discrete and dimensional representations of emotions, these representations do not fully reconcile with recent neuroscience studies that increasingly suggest a multi-process mechanism underlying emotional experience. Moreover, the latter view accords with psychological theories that consider emotions as multicomponent phenomena, such as appraisal theories. Although there is no complete consensus on the specific components of emotions and fundamental principles defining their organization, the Component Process Model (CPM) is well established framework describing an emotion as a dynamic process with five major highly interrelated components: cognitive appraisal, expression, motivation, physiology and feeling. Yet, few studies have systematically investigated a range of discrete emotions through this full multi-componential view. In the present study, we therefore elicited various emotions during movie watching and measured their manifestation across these components. Our primary goal was to investigate the relationship between physiological measures and the theoretically defined components of emotions. In addition, we also investigated whether discrete emotions could be predicted from information provided by the multicomponent response patterns, as well as the specific contributions of each component in such predictions. Results suggest that physiological features are interrelated to all other components of emotion, but the least significant predictors for emotion classification. Overall, emotion prediction was significantly higher when classifiers were trained with all five components. The findings therefore support a description of emotion as a dynamic multicomponent process, in which the emergence of a conscious feeling state requires the integration of all the components.
The neuroblast timer genenubbinexhibits functional redundancy with gap genes to regulate segment identity inTribolium
Authors: Tidswell Olivia RA , Benton Matthew A , Akam Michael E
Published: April 2021

InDrosophila, segmentation genes of the gap class form a regulatory network that positions segment boundaries and assigns segment identities. This gene network shows striking parallels with another gene network known as the neuroblast timer series. The neuroblast timer geneshunchback, Krüppel, nubbin,andcastorare expressed in temporal sequence in neural stem cells to regulate the fate of their progeny. These same four genes are expressed in corresponding spatial sequence along theDrosophilablastoderm. The first two,hunchbackandKrüppel, are canonical gap genes, butnubbinandcastorhave limited or no roles inDrosophilasegmentation. Whethernubbinandcastorregulate segmentation in insects with the ancestral, sequential mode of segmentation remains largely unexplored.

We have investigated the expression and functions ofnubbinandcastorduring segment patterning in the sequentially-segmenting beetleTribolium. Using multiplex fluorescentin situhybridisation, we show thatTc-hunchback,Tc-Krüppel,Tc-nubbinandTc-castorare expressed sequentially in the segment addition zone ofTribolium, in the same order as they are expressed inDrosophilaneuroblasts. Furthermore, simultaneous disruption of multiple genes reveals thatTc-nubbinregulates segment identity, but does so redundantly with two previously described gap/gap-like genes,Tc-giantandTc-knirps. Knockdown of two or more of these genes results in the formation of up to seven pairs of ectopic legs on abdominal segments. We show that this homeotic transformation is caused by loss of abdominal Hox gene expression, likely due to expandedTc-Krüppelexpression. Our findings support the theory that the neuroblast timer series was co-opted for use in insect segment patterning, and contribute to our growing understanding of the evolution and function of the gap gene network outside ofDrosophila.
Resilience of riparian vegetation composition and diversity following cessation of livestock grazing in northeastern Oregon
Authors: Kauffman J Boone , Coleman Greg , Otting Nick , Lytjen Danna , Nagy Dana , Beschta Robert L.
Published: April 2021

Riparian ecosystem restoration has been accomplished through exclusion of livestock using corridor fencing along hundreds of kilometers of streams in the western USA, for the benefit of riparian-obligate wildlife and endangered fishes. Yet few studies have evaluated shifts in the vegetation composition and diversity following the cessation of livestock impacts. We sampled riparian vegetation composition along 11-paired grazed and ungrazed (exclosed) stream reaches in northeastern Oregon, USA. Exclosure ages ranged from 2 to >30 years and grazing treatments varied from light grazing every one out of three years to heavy season-long grazing. Species richness and diversity was higher in the ungrazed reaches (p =0.002). The abundance of native sedges (Carexspp.) and broad-leaved forbs were also significantly (p < 0.05) greater in ungrazed areas. In contrast, exotic species adapted to grazing such asPoa pratensisandTrifolium repenswere more abundant in grazed stream reaches. The prevalence of hydrophytic species significantly increased (p ≤ 0.01) in ungrazed reaches, (based on wetland species indicator scores), indicating that wetland-dominated communities within the ungrazed stream reaches were replacing ones adapted to drier environments. The increased abundance of facultative and wetland-obligate species in ungrazed reaches compared to grazed reaches suggests that livestock grazing exacerbates those climate change effects also leading to warmer and drier conditions. Further, riparian-obligate shrub cover along the streambank was higher in 7 of 8 exclosures that were older than 5 years. As a restoration approach the inherent resilience of riparian ecosystems exhibited in ungrazed riparian zones suggest positive feedbacks to other beneficial ecosystem processes such as increased species and habitat diversity, increased carbon sequestration, enhanced allochthonous inputs and greater sediment retention, that would affect the aquatic and terrestrial biota, water quality, and stream morphology.
Characterization of light penetration through brain tissue, for optogenetic stimulation
Authors: Johnson Emily L. , Walsh Darren , Hutchings Frances , Palmini Rolando Berlinguer , Ponon Nikhil , O’Neill Anthony , Jackson Andrew , Degenaar Patrick , Trevelyan Andrew J.
Published: April 2021

The recent development of optogenetic tools, to manipulate neuronal activity using light, provides opportunities for novel brain-machine interface (BMI) control systems for treating neurological conditions. An issue of critical importance, therefore, is how well light penetrates through brain tissue. We took two different approaches to estimate light penetration through rodent brain tissue. The first employed so-called “nucleated patches” from cells expressing the light-activated membrane channel, channelrhodopsin (ChR2). By recording light-activated currents, we used these nucleated patches as extremely sensitive, microscopic, biological light-meters, to measure light penetration through 300-700µm thick slices of rodent neocortical tissue. The nucleated patch method indicates that the effective illumination drops off with increasing tissue thickness, corresponding to a space constant of 317µm (95% confidence interval between 248-441µm). We compared this with measurements taken from directly visualizing the illumination of brain tissue, orthogonal to the direction of the light. This yielded a contour map of reduced illumination with distance, which along the direction of light delivery, had a space constant,τ453µm. This yields a lower extinction coefficient, µe(the reciprocal ofτ, ∼3mm-1) than previous estimates, implying better light penetration from LED sources than these earlier studies suggest.
Quantitative mapping of cerebral oxygen metabolism using breath-hold calibrated fMRI
Authors: Germuska M , Stickland RC , Chiarelli AM , Chandler HL , Wise RG
Published: April 2021

Magnetic resonance imaging (MRI) offers the possibility to non-invasively map the rate of cerebral metabolic oxygen consumption (CMRO2), which is essential for understanding and monitoring neural function in both health and disease. Existing methods of mapping CMRO2, based on respiratory modulation of arterial spin labelling (ASL) and blood oxygen level dependent (BOLD) signals, require lengthy acquisitions and independent modulation of both arterial oxygen and carbon dioxide levels. Here, we present a new simplified method for mapping the rate of cerebral oxygen metabolism that can be performed using a simple breath-holding paradigm. The method incorporates flow-diffusion modelling of oxygen transport and physiological constraints to create a non-linear mapping between the maximum BOLD signal, M, baseline blood flow (CBF0), and CMRO2. A gradient boosted decision tree is used to learn this mapping directly from simulated MRI data. Modelling studies demonstrate that the proposed method is robust to variation in cerebral physiology and metabolism. This new gas-free methodology offers a rapid and pragmatic alternative to existing dual-calibrated methods, removing the need for specialist respiratory equipment and long acquisition times. In-vivo testing of the method, using an 8-minute 45 second protocol of repeated breath-holding, was performed on 15 healthy volunteers, producing quantitative maps of cerebral blood flow (CBF), oxygen extraction fraction (OEF), and CMRO2.
Assessing bivalve phylogeny using Deep Learning and Computer Vision approaches
Authors: Kiel Steffen
Published: April 2021

Phylogenetic analyses using morphological data currently require hand-crafted character matrices, limiting the number of taxa that can be included. Here I explore how Deep Learning and Computer Vision approaches typically applied to image classification tasks, may be used to infer phylogenetic relationships among bivalves. A convolutional neural network (CNN) was trained on thousands of images showing species of 75 bivalve families. The predictions of the CNN on a large number of bivalve images are then interpreted as an indication of how similar these bivalves are to each other, are averaged by the families to which the species belonged, and visualized in a cluster diagram. In this cluster diagram, significantly more families clustered with members of their subclasses than expected by chance, confirming the feasibility of the approach. To address the issue of convergent evolution, two further CNNs were trained, on the same images but grouped by the orders and subclasses to which the species belonged. Combining predictions for the same images but on different taxonomic levels improved the inferred phylogenetic relationships also of families that the CNNs had not been trained on. Finally, this combined tree is merged with five published phylogenetic trees into a supertree, representing the largest single phylogeny of the Bivalvia to date, encompassing 128 families, including six exclusively fossil families and nine extant families for which presently no molecular data are available. Issues inherent to the approach and suggestions for future directions are discussed.
Natural Image Statistics for Mouse Vision
Authors: Abballe Luca , Asari Hiroki
Published: April 2021

The mouse has dichromatic color vision based on two different types of opsins: short (S)- and middle (M)-wavelength-sensitive opsins with peak sensitivity to ultraviolet (UV; 360 nm) and green light (508 nm), respectively. In the mouse retina, cone photoreceptors that predominantly express the S-opsin are more sensitive to contrasts and denser towards the ventral retina, preferentially sampling the upper part of the visual field. In contrast, the expression of the M-opsin gradually increases towards the dorsal retina that encodes the lower visual field. Such a distinctive retinal organization is assumed to arise from a selective pressure in evolution to efficiently encode the natural scenes. However, natural image statistics of UV light remain largely unexplored. Here we developed a multi-spectral camera to acquire high-quality UV and green images of the same natural scenes, and examined the optimality of the mouse retina to the image statistics. We found that the local contrast and the spatial correlation were both higher in UV than in green for images above the horizon, but lower in UV than in green for those below the horizon. This suggests that the dorsoventral functional division of the mouse retina is not optimal for maximizing the bandwidth of information transmission. Factors besides the coding efficiency, such as visual behavioral requirements, will thus need to be considered to fully explain the characteristic organization of the mouse retina.
Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq
Authors: Fustero-Torre Coral , Jiménez-Santos María José , García-Martín Santiago , Carretero-Puche Carlos , García-Jimeno Luis , Di Domenico Tomás , Gómez-López Gonzalo , Al-Shahrour Fátima
Published: April 2021

We present Beyondcell (https://gitlab.com/bu_cnio/beyondcell/), a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments. Our method calculates an enrichment score in a collection of drug signatures, delineating therapeutic clusters (TCs) within cellular populations. Additionally, Beyondcell determines therapeutic differences among cell populations, and generates a prioritised ranking of the differential sensitivity drugs between chosen conditions to guide drug selection. We performed Beyondcell analysis in four single-cell datasets to validate our score and to demonstrate that TCs can be exploited to target malignant cells both in cancer cell lines and tumour patients.
Naïve individuals promote collective exploration in homing pigeons
Authors: Valentini Gabriele , Pavlic Theodore P. , Walker Sara Imari , Pratt Stephen C. , Biro Dora , Sasaki Takao
Published: April 2021

Group-living animals that rely on stable foraging or migratory routes can develop behavioural traditions to pass route information down to inexperienced individuals. Striking a balance between exploitation of social information and exploration for better alternatives is essential to prevent the spread of maladaptive traditions. We investigated this balance during cumulative route development in the homing pigeonColumba livia. We quantified information transfer within pairs of birds in a transmission-chain experiment and determined how birds with different levels of experience contributed to the exploration– exploitation trade-off. Newly introduced naïve individuals were initially more likely to initiate exploration than experienced birds, but the pair soon settled into a pattern of alternating leadership with both birds contributing equally. Experimental pairs showed an oscillating pattern of exploration over generations that might facilitate the discovery of more efficient routes. Our results introduce a new perspective on the roles of leadership and information pooling in the context of collective learning.
Radiation exposure of the base of the heart accelerates coronary atherosclerosis
Authors: Nepali Prerna R. , Mathieu Mickael , Kitz Sarah , Nakauchi Chiharuko , Gabriels Karen , Russell James , Monette Sebastien , te Poele Johannes A. , Heeneman Sylvia , Rimner Andreas , Qiu Yunping , Kurland Irwin J. , Stewart Fiona A. , Jaimes Edgar A. , Haimovitz-Friedman Adriana
Published: April 2021

Clinical studies have identified cardiac exposure as an independent predictor for cardiovascular mortality in patients treated with radiation therapy (RT) for thoracic malignancies. Although the mechanisms are not completely understood, the available evidence indicate that direct injury to the coronary arteries endothelium is implicated. In these studies we tested the hypothesis that different areas of the heart are more sensitive to the effects of RT on the formation of atherosclerotic plaque in apolipoprotein E deficient (ApoE-/-) mice, a well validated model of atherosclerosis.

Methods

ApoE-/-mice on a high fat diet (HFD) received 16Gy cardiac irradiation targeted to the whole or partial (apical or basal) region of the heart at 9 weeks or 16 weeks of age. Atherosclerotic lesions and inflammatory changes in the hearts as compared to control unirradiated mice were assessed eight weeks following radiation.

Results

After either basal or whole heart RT at 9 weeks of age the number of subendocardial atherosclerotic lesions at the heart base was higher as compared to unirradiated mice. Irradiation of the apex did not increase the number of subendocardial atherosclerotic lesions in any region. After basal RT at 16 weeks of age the number of coronary and subendocardial atherosclerotic lesions was higher as compared to controls. Neither apical or whole heart RT had an impact on the development or acceleration of lesions in the basal region of the hearts of 16 week old mice, thus demonstrating the adverse impact of basal irradiation. Infiltration of inflammatory cells (CD45+and CD3+) and enhanced expression of endothelial adhesion molecules (CD31), were differentially and locally regulated based upon the site of irradiation. In support of a role of eicosanoid mediators for base or whole heart atherogenic irradiation effects, apex irradiation eicosanoid mediators are not clearly atherogenic, in contrast to eicosanoid mediators detected in serum after base heart irradiation. These results indicate that the base of the heart is significantly more prone to the development of atherosclerotic lesions in the coronary arteries post-RT.

Conclusion

Our results indicate that the base of the heart is more susuceptible to development of RT-induced atherosclerotic lesions and therefore avoidance from RT direct exposure to this area may reduce the risk for atherosclerotic disease in patients undergoing RT.
A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression
Authors: Chang Ni-Chen , Rovira Quirze , Wells Jonathan N. , Feschotte Cédric , Vaquerizas Juan M.
Published: April 2021

There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos, and by the relative scarcity of active TEs in these organisms. Zebrafish is an outstanding model for the study of vertebrate development and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2,000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whilst short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. While two thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched amongst transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides an important resource for using zebrafish as a model to study the impact of TEs on vertebrate development.
Emergent myxobacterial behaviors arise from reversal suppression induced by kin contacts
Authors: Balagam Rajesh , Cao Pengbo , Sah Govind P. , Zhang Zhaoyang , Subedi Kalpana , Wall Daniel , Igoshin Oleg A.
Published: April 2021

A wide range of biological systems – from microbial swarms to bird flocks, display emergent behaviors driven by coordinated movement of individuals. To this end, individual organisms interact by recognizing their kin and adjusting their motility based on others around them. However, even in the best-studied systems, the mechanistic basis of the interplay between kin recognition and motility coordination is not understood. Here, using a combination of experiments and mathematical modeling, we uncover the mechanism of an emergent social behavior inMyxococcus xanthus. By overexpressing cell surface adhesins, TraA and TraB, involved in kin recognition, large numbers of cells adhere to one another and form organized macroscopic circular aggregates that spin clockwise or counterclockwise. Mechanistically, TraAB adhesion results in sustained cell-cell contacts that trigger cells to suppress cell reversals, and circular aggregates form as the result of cells’ ability to follow their own cellular slime trails. Furthermore, ourin-silicosimulations demonstrate a remarkable ability to predict self-organization patterns when phenotypically distinct strains are mixed. For example, defying naïve expectations, both models and experiments found that strains engineered to overexpress different and incompatibletraABallelles nevertheless form mixed circular aggregates. Therefore, this work provides key mechanistic insights intoM. xanthussocial interactions and demonstrates how local cell contacts induce emergent collective behaviors by millions of cells.

Importance

In many species, large populations exhibit emergent behaviors whereby all related individuals move in unison. For example, fish in schools can all dart in one direction simultaneously to avoid a predator. Currently, it is impossible to explain how such animals recognize kin through brain cognition and elicit such behaviors at a molecular level. However, microbes also recognize kin and exhibit emergent collective behaviors that are experimentally tractable. Here, using a model social bacterium, we engineer dispersed individuals to organize into synchronized collectives that create emergent patterns. With experimental and mathematical approaches we explain how this occurs at both molecular and population levels. The results demonstrate how the combination of local physical interactions triggers intracellular signaling, which in turn leads to emergent behavior on a population scale.
A repurposed drug screen identifies compounds that inhibit the binding of the COVID-19 spike protein to ACE2
Authors: Tsegay Kaleb B. , Adeyemi Christiana M. , Gniffke Edward P. , Sather D. Noah , Walker John K. , Smith Stephen E. P.
Published: April 2021

Repurposed drugs that block the interaction between the SARS-CoV-2 spike protein and its receptor ACE2 could offer a rapid route to novel COVID-19 treatments or prophylactics. Here, we screened 2701 compounds from a commercial library of drugs approved by international regulatory agencies for their ability to inhibit the binding of recombinant, trimeric SARS-CoV-2 spike protein to recombinant human ACE2. We identified 56 compounds that inhibited binding by <90%, measured the EC50of binding inhibition, and computationally modeled the docking of the best inhibitors to both Spike and ACE2. These results highlight an effective screening approach to identify compounds capable of disrupting the Spike-ACE2 interaction as well as identifying several potential inhibitors that could serve as templates for future drug discovery efforts.