bluuebunny/crossref_metadata_2025 huggingface dataset:
Personal bias in nutrition advice: A survey of healthcare professionals’ recommendations regarding dairy and plant-based dairy alternatives
Authors: Clark Bridget E. , Pope Lizzy , Belarmino Emily H.
Published: July 2021

Objective

To examine the relationship between health professionals’ personal dietary preferences and their professional nutrition advice on dairy and plant-based dairy alternatives.

Design

Cross sectional web-based survey. Survey examined health professionals’ personal dietary preferences, including milk preference, (plant-based or dairy milk), dietary pattern (vegetarian or omnivore), and if they followed a “plant-based” diet, and examined if they would advise patients to consume dairy and/or plant-based dairy alternatives. Logistic regression models examined if health professionals’ personal dietary preferences were associated with their willingness to recommend either product.

Setting

Sample of U.S. health professionals.

Participants

Non-probability convenience sampling recruited registered dietitian nutritionists, physicians, physician assistants, nurse practitioners, registered nurses, licensed practical nurses, dentists, dental hygienists, and students in any of these degree programs holding Junior standing and above. 331 respondents completed relevant survey questions and were included in analyses.

Results

Most respondents would recommend dairy (81%) and dairy alternatives (72%) to their patients. Half (49%) reported a preference for plant-based milk, about 40% identified as having a dietary pattern that reduces animal product intake, and about 40% reported following a plant-based dietary pattern. Plant-based milk preference (OR 4.52; 95% CI 2.31 to 8.82,p<0.001) and following a vegetarian dietary pattern (OR 1.91; 95% CI 1.11 to 3.27,p=0.019) were associated with greater odds of recommending dairy alternatives to a patient. Plant-based milk preference (OR 0.16; 95% CI 0.07 to 0.35,p<0.001), following a vegetarian dietary pattern (OR 0.45; 95% CI 0.25 to 0.82,p=0.009), and following a plant-based dietary pattern (OR 0.41; 95% CI 0.22 to 0.76,p=0.005) were associated with lessor odds of recommending dairy to a patient. Dietetics professionals were more likely than all other health professionals to recommend both dairy and dairy alternatives to patients.

Conclusions

Healthcare professionals’ nutrition recommendations appear to reflect their personal nutrition habits, despite dairy being an important source of essential nutrients for patients who are willing and able to consume it. Improved nutrition training focusing on evidence-based nutrition recommendations, reducing personal bias in practice, and routinely including registered dietitians on interprofessional healthcare teams may improve the quality of nutrition advice given to U.S. consumers.
Cornering an Ever-Evolving Coronavirus: TATX-03, a fully human synergistic multi-antibody cocktail targeting the SARS-CoV-2 Spike Protein with in vivo efficacy
Authors: Roodink Ilse , van Erp Maartje , Li Andra , Potter Sheila , van Duijnhoven Sander M J , Kuipers Arthur J , Kazemier Bert , van Geffen Ellen , Hemrika Wieger , Berkeveld Bob , Sonnemans Glenn , de Vries Britte S , Boers Bianca , Smits Milou , Meurs Sanne , de Pooter Maaike , Thom Alexandra , Duplantis Barry N , Romijn Roland A , Houser Jeremy , Bath Jennifer , Abdiche Yasmina N
Published: July 2021

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created an ongoing global human health crisis and will likely become endemic, requiring novel sustainable therapeutic strategies. We report on the discovery of a fully human multi-antibody cocktail (TATX-03) targeting diversified non-overlapping epitopes on the SARS-CoV-2 spike protein that suppressed replication-competent viral titers to undetectable levels in the lungs of SARS-CoV-2 challenged hamsters upon both prophylactic and therapeutic administration. While monotherapy with two of the individual cocktail components also showed clear in vivo protection, neither recapitulated the efficacy of TATX-03. This synergistic effect was further supported by examining in vivo efficacy of these individual antibodies and corresponding combination therapy at a lower dose. Furthermore, in vitro screenings using VSV-particles pseudo-typed with spike proteins representing the SARS-CoV-2 variants of concern Alpha, Beta, and Delta showed that TATX-03 maintained its neutralization potency. These results merit further development of TATX-03 as a potential therapy for SARS-CoV-2 infection with resistance to mutagenic escape.
Remodeling of ryanodine receptor isoform 1 channel regulates the sweet and umami perception of Rattus norvegicus
Authors: Wang Wenli , Lu Dingqiang , Xu Qiuda , Jin Yulian , Gang Guangchang , Liu Yuan
Published: July 2021

Sweet and umami are respectively elicited by sweet/umami receptor on the tongue and palate epithelium. However, the molecular machinery allowing to taste reaction remains incompletely understood. Through a phosphoproteomic approach, we found the key proteins that trigger taste mechanisms based on the phosphorylation cascades. Thereinto, ryanodine receptor isoform 1 (RYR1) was further verified by sensor and behaviors assay. A model proposing RYR1-mediated sweet/umami signaling: RYR1 channel which mediates Ca2+ release from the endoplasmic reticulum is closed by its dephosphorylation in the bud tissue after umami/sweet treatment. And the alteration of Ca2+ content in the cytosol induces a transient membrane depolarization and generates cell current for taste signaling transduction. We demonstrate that RYR1 is a new channel in regulation of sweet/umami signaling transduction and also propose a “metabolic clock” notion based on sweet/umami sensing. Our study provides a rich fundamental for a system-level understanding of taste perception mechanism.
Expression patterns of Arc mRNA after renewal of appetitive behavior in female rats
Authors: Hilz Emily N , Agee Laura A. , Jun Donyun , Monfils Marie H , Lee Hongjoo J.
Published: July 2021

Renewal of appetitive behavior depends on the gonadal hormonal state of the female rat. In this experiment the effect of female rat estrous cycle stage on renewal of appetitive behaviors is replicated and extended upon to understand how endogenous hormonal states around the estrous cycle drive renewal at the neuronal population level. Estrous cycle stage (i.e., proestrus (P, high hormone) or metestrus/diestrus (M/D, low hormone)) was considered during two important learning and behavioral expression windows: at extinction training and during LTM/renewal testing. First, rats in P during context-dependent extinction training but in some other stage of the estrous cycle during long-term memory and renewal testing (Different) were shown to exhibit more renewal of conditioned foodcup (but not conditioned orienting) behavior compared to rats in other estrous cycle groups. Next, cellular compartment analysis of temporal activity using fluorescence in situ hybridization (catFISH) was used to examine immediate early gene activity of Arc mRNA in neuronal populations after distinct context-stimulus exposures (i.e., extinction and acquisition test contexts). Arc mRNA expression patterns were examined in the prefrontal cortex (PFC), amygdala, hippocampus (HPC), and paraventricular nucleus of the thalamus. P-different rats showed differential neuronal population activity in the infralimbic cortex of the PFC, the lateral amygdaloid nucleus, and both CA1 and CA3 regions of the dorsal HPC. In each region P-different rats exhibited more co-expression and less specificity of Arc mRNA compared to other hormonal groups, indicating that renewal of appetitive foodcup behavior induces Arc mRNA in overlapping neuronal populations in female rats.
Early life exposure to high fructose diet induces metabolic dysregulation associated with sex-specific cognitive impairment in adolescent rats
Authors: Barrett Catherine E , Jiang Megan , O’Flaherty Brendan G , Dias Brian , Rainnie Donald G , Young Larry J , Menigoz Aurelie
Published: July 2021

Background

The incidence of adolescent mental health disorders is on the rise. Epidemiological studies suggest that poor nutrition is a significant contributor to this public health crisis, specifically through exposure to high level of dietary sugar, including fructose, during critical periods of development. Previous studies have shown that elevated fructose exposure during adolescence disrupts mental health. Further, it seems that infants display the highest level of exposure to fructose based on nutritional surveys. Despite these data, it is currently unknown how fructose exposure, specifically during infancy, may impact adolescent mental health.

Methods

We developed an experimental protocol in rats to investigate the effects of fructose exposure during infancy on behavioral, cognitive and metabolic endpoints in adolescence. Specifically, rat pups were exposed to fructose from birth until weaning through maternal diet. Metabolic assays, quantitative PCR and behavioral protocols such as open field, elevated O maze and a Go/ No-Go operant task, were used to determine whether high fructose exposure during infancy may set the stage for behavioral and metabolic dysfunction in adolescence.

Results

We found that exposing rats to high fructose from birth to weaning resulted in higher circulating glucose, insulin and leptin levels in adolescence. High fructose during infancy also increased bodyweight, disrupted metabolic homeostasis in the basolateral amygdala (BLA) as indicated by decreased activity of the cellular energy sensor AMPK, and impaired attention and impulsivity in a male-specific manner. This impaired attention observed in adolescent male rats following neonatal fructose exposure was partially rescued by viral-mediated,in vivoexpression of a constitutively active form of AMPK in principal neurons of the BLA.

Conclusion

Our results suggest that exposure to high level of fructose during infancy may impact adolescent mental health in a male-specific manner and that manipulation of AMPK activity may mitigate this impact.
Forearm and hand muscles exhibit high coactivation and overlapping of cortical motor representations
Authors: Tardelli Gabriela P. , Souza Victor Hugo , Matsuda Renan H. , Garcia Marco A. C. , Novikov Pavel A. , Nazarova Maria A. , Baffa Oswaldo
Published: July 2021

Most of the motor mapping procedures using navigated transcranial magnetic stimulation (nTMS) follow the conventional somatotopic organization of the primary motor cortex (M1) by assessing the representation of a particular target muscle, disregarding the possible coactivation of synergistic muscles. In turn, multiple reports describe a functional organization of the M1 with an overlapping among motor representations acting together to execute movements. In this context, the overlap degree among cortical representations of synergistic hand and forearm muscles remains an open question. This study aimed to evaluate the muscle coactivation and representation overlapping common to the grasping movement and its dependence on the stimulation parameters. The nTMS motor maps were obtained from one carpal muscle and two intrinsic hand muscles during rest. We quantified the overlapping motor maps in size (area and volume overlap degree) and topography (similarity and centroid’s Euclidean distance) parameters. We demonstrated that these muscle representations are highly overlapped and similar in shape. The overlap degrees involving the forearm muscle were significantly higher than only among the intrinsic hand muscles. Moreover, the stimulation intensity had a stronger effect on the size compared to the topography parameters. Our study contributes to a more detailed cortical motor representation towards a synergistic, functional arrangement of M1. Understanding the muscle group coactivation may provide more accurate motor maps when delineating the eloquent brain tissue during pre-surgical planning.
Timing of water limitations affects source to sink differences in δ13C composition in apple
Authors: Kalcsits Lee , Valverdi Nadia , Reid Michelle
Published: July 2021

Deficit irrigation is used to reduce vegetative vigor, increase fruit quality, and conserve water resources. However, physiological responses to deficit irrigation can vary depending on soil and environmental conditions. Although physiological measurements are often made at single points in time, responses are often longer lasting and a measurement that integrates responses over time would have greater value in assessing the effectiveness of deficit irrigation practices. Carbon isotope composition has long been used as a proxy measurement for water-use efficiency, stomatal conductance, and carbon dioxide exchange with the atmosphere and is heavily influenced by water status. Potentially, fruit, leaves, or other tissues could be used as samples for carbon isotope measurements. However, it is not well known how irrigation practices can influence both source and sink tissue carbon isotope composition in perennial systems. Here, we used two experiments to determine how irrigation timing affects both source and sink δ13C at the end of the season. Irrigation limitations were initiated after bloom for either the whole season or for early, middle, or late season and compared to a well-watered control. For both experiments, leaves were poor indicators of irrigation deficit treatments that were applied during the season. There were no significant differences in leaf δ13C between deficit treatments and the control for both experiments. However, all sink tissues including roots and stems in experiment one for both years and for fruits in experiment two for both years were significantly more enriched compared to the well-watered control. Environmental conditions during the season also appeared to influence the magnitude of difference in δ13C between deficit irrigation treatments and the control. These results indicate that the use of sink tissues are more sensitive for measuring signals associated with in-season water deficits. Carbon isotope composition can be an effective proxy to measure efficacy of irrigation treatments at the physiological level.
Functional interactomes of the Ebola virus polymerase identified by proximity proteomics in the context of viral replication
Authors: Fang Jingru , Pietzsch Colette , Tsaprailis George , Crynen Gogce , Cho Kelvin Frank , Ting Alice Y. , Bukreyev Alexander , de la Torre Juan Carlos , Saphire Erica Ollmann
Published: July 2021

Ebola virus (EBOV) critically depends on the viral polymerase to replicate and transcribe the viral RNA genome in the cytoplasm of host cells, where cellular factors can antagonize or facilitate the virus life cycle. Here we leveraged proximity proteomics and conducted an siRNA screen to define the functional interactome of EBOV polymerase. As proof-of-principle, we validated two cellular mRNA decay factors from 35 identified host factors: eukaryotic peptide chain release factor subunit 3a (eRF3a/GSPT1) and up-frameshift protein 1 (UPF1). Our data suggest that EBOV can subvert restrictions of cellular mRNA decay and repurpose both GSPT1 and UPF1 to promote viral replication. Treating EBOV-infected human hepatocytes with a drug candidate that targets GSPT1 for degradation significantly reduced viral RNA load and particle production. Our work demonstrates the utility of proximity proteomics to capture the functional host-interactome of the EBOV polymerase and to illuminate host-dependent regulations of viral RNA synthesis.
The Remote Assessment of Parkinsonism Supporting Ongoing Development of Interventions in Gaucher Disease – Study Protocol
Authors: Higgins Abigail Louise , Toffoli Marco , Mullin Stephen , Lee Chiao-Yin , Koletsi Sofia , Avenali Micol , Blandini Fabio , Schapira Anthony H V
Published: July 2021

Mutations in GBA which are causative of Gaucher disease in their biallelic form, are the most common genetic risk factor for Parkinson disease. The diagnosis of Parkinson disease relies upon clinically defined motor features which appear after irreversible neurodegeneration. Prodromal symptoms of Parkinson disease may provide a means to predict latent pathology, years before the onset of motor features. Previous work has reported prodromal features of Parkinson disease in GBA mutation carriers, however this has been insufficiently sensitive to identify those that will develop Parkinson disease. The Remote Assessment of Parkinsonism Supporting Ongoing Development of Interventions in Gaucher Disease (RAPSODI) study assesses a large cohort of GBA mutation carriers, to aid development of procedures for earlier diagnosis of Parkinson disease.

Summary Points

The therapeutic focus for Parkinson disease is currently symptomatic, rather than disease-modifying or neuroprotective.

Non-motor prodromal features of Parkinson disease may precede the motor symptoms required for clinical diagnosis by several years.

GBAmutations, which are associated with Gaucher disease in their biallelic form, have emerged as the most common genetic risk factor for Parkinson Disease.

GBAassociated PD displays a slightly exaggerated phenotype, including earlier age of onset, enhanced cognitive decline, more severe affective disturbances, and a greater likelihood of manifesting REM Sleep Behaviour Disorder, hyposmia and autonomic dysfunction.

The RAPSODI GD study is an annual remote assessment which aims to define the clinical prodrome of PD in a large cohort ofGBAmutation carriers, to accurately predict clinical diagnosis.

The secondary objectives of RAPSODI GD are to risk stratify homozygote and heterozygoteGBAmutation carriers for PD risk, understand the variable penetrance of theGBAassociated PD phenotype, and create a platform for the future evaluation of biomarkers of disease.

The putative implication of the RAPSODI GD study is to contribute towards earlier diagnosis ofGBAassociated PD, to provide a timeframe for delivering neuroprotective interventions.

Defining prodromal PD inGBAcarriers may have wider implications for sporadic PD.
Mixed culture metagenomics of the microbes making sour beer
Authors: Araujo Piraine Renan Eugênio , Leivas Leite Fábio Pereira , Bochman Matthew L.
Published: July 2021

Mixed microbial cultures create sour beers, but many brewers do not know which microbes comprise their cultures. The objective of this work was to use deep sequencing to identify microorganisms in sour beers brewed by spontaneous and non-spontaneous methods. Twenty samples were received from brewers, which were processed for microbiome analysis by next generation sequencing. For bacteria, primers were used to amplify the V3-V4 region of the 16S rRNA gene; fungal DNA detection was performed using primers to amplify the entire internal transcribed spacer region. The sequencing results were then used for taxonomy assignment, sample composition, and diversity analyses, as well as nucleotide BLAST searching. We identified 60 genera and 140 species of bacteria, of which the most prevalent wereLactobacillus acetotolerans, Pediococcus damnosus, andRalstonia picketti/mannitolilytica. In fungal identification, 19 genera and 26 species were found, among which the most common yeasts wereBrettanomyces bruxellensisandSaccharomyces cerevisiae. In some cases, genetic material from more than 60 microorganisms was found in a single sample. In conclusion, we were able to determine the microbiomes of various mixed cultures used to produce beer, providing useful information to better understand the sour beer fermentation process and brewing techniques.
Colistin resistance in Escherichia coli confers protection of the cytoplasmic but not outer membrane from the polymyxin antibiotic
Authors: Humphrey Madeleine , Larrouy-Maumus Gerald J. , Furniss R. Christopher D. , Mavridou Despoina A. I. , Sabnis Akshay , Edwards Andrew M.
Published: July 2021

Colistin is a polymyxin antibiotic of last resort for the treatment of infections caused by multi-drug resistant Gram-negative bacteria. By targeting lipopolysaccharide (LPS), the antibiotic disrupts both the outer and cytoplasmic membranes, leading to lysis and bacterial death. Colistin resistance in Escherichia coli occurs via mutations in the chromosome or the acquisition of mobilised colistin resistance (mcr) genes. Both these colistin resistance mechanisms result in chemical modifications to the LPS, with positively charged moieties added at the cytoplasmic membrane before the LPS is transported to the outer membrane. We have previously shown that MCR-1-mediated LPS modification protects the cytoplasmic but not the outer membrane from damage caused by colistin, enabling bacterial survival. However, it remains unclear whether this observation extends to colistin resistance conferred by other mcr genes, or resistance due to chromosomal mutations. Using a panel of clinical E. coli that had acquired mcr -1, -1.5, -2, -3, -3.2 or -5, or had acquired polymyxin resistance independently of mcr genes, we found that almost all isolates were susceptible to colistin-mediated permeabilisation of the outer, but not cytoplasmic, membrane. Furthermore, we showed that permeabilisation of the outer membrane of colistin resistant isolates by the polymyxin is in turn sufficient to sensitise bacteria to the antibiotic rifampicin, which normally cannot cross the LPS monolayer. These findings demonstrate that colistin resistance in E. coli is typically due to protection of the cytoplasmic but not outer membrane from colistin-mediated damage, regardless of the mechanism of resistance.
Lineage-specific regulatory changes in the pathological cardiac remodeling of hypertrophy cardiomyopathy unraveled by single-nucleus RNA-seq and spatial transcriptomics
Authors: Liu Xuanyu , Yin Kunlun , Chen Liang , Chen Wen , Li Wenke , Zhang Taojun , Sun Yang , Yuan Meng , Wang Hongyue , Wang Shuiyun , Hu Shengshou , Zhou Zhou
Published: July 2021

BACKGROUND

Hypertrophy cardiomyopathy (HCM) is the most common cardiac genetic disorder with the histopathological features of cardiomyocyte hypertrophy and cardiac fibrosis. The pathological remodeling that occurs in the myocardium of HCM patients may ultimately progress to heart failure and death. A thorough understanding of the cell type-specific changes in the pathological cardiac remodeling of HCM is crucial for developing successful medical therapies to prevent or mitigate the progression of this disease.

METHODS

We performed single-nucleus RNA-seq of the cardiac tissues from 10 HCM patients and 2 healthy donors, and conducted spatial transcriptomic assays of 4 cardiac tissue sections from 3 HCM patients. Comparative analyses were performed to explore the lineage-specific changes in expression profile, subpopulation composition and intercellular communication in the cardiac tissues of HCM patients. Based on the results of independent analyses including pseudotime ordering, differential expression analysis, and differential regulatory network analysis, we prioritized candidate therapeutic targets for mitigating the progression to heart failure or attenuating the cardiac fibrosis in HCM. Using the spatial transcriptomic data, we examined the spatial activity patterns of the key candidate genes, pathways and subpopulations.

RESULTS

Unbiased clustering of 55,122 nuclei from HCM and healthy conditions revealed 9 cell lineages and 28 clusters. Significant expansion of vascular-related lineages and contraction of cardiomyocytes, fibroblasts and myeloid cells in HCM were observed. The transcriptomic dynamics during the transition towards the failing state of cardiomyocytes in HCM were uncovered. Candidate target genes for mitigating the progression to heart failure in HCM were obtained such asFGF12,IL31RA,BDNF,S100A1,CRYABandPROS1. The transcriptomic dynamics underlying the fibroblast activation were also uncovered, and candidate targets for attenuating the cardiac fibrosis in HCM were obtained such asRUNX1,MEOX1,AEBP1,LEF1andNRXN3.

CONCLUSIONS

We provided a comprehensive analysis of the lineage-specific regulatory changes in HCM. Our analysis identified a vast array of candidate therapeutic target genes and pathways to prevent or attenuate the pathological remodeling of HCM. Our datasets constitute a valuable resource to examine the lineage-specific expression changes of HCM at single-nucleus and spatial resolution. We developed a web-based interface (http://snsthcm.fwgenetics.org/) for further exploration.
Fixation probabilities in network structured meta-populations
Authors: Yagoobi Sedigheh , Traulsen Arne
Published: July 2021

The effect of population structure on evolutionary dynamics is a long-lasting research topic in evolutionary ecology and population genetics. Evolutionary graph theory is a popular approach to this problem, where individuals are located on the nodes of a network and can replace each other via the links. We study the effect of complex network structure on the fixation probability, but instead of networks of individuals, we model a network of sub-populations with a probability of migration between them. We ask how the structure of such a meta-population and the rate of migration affect the fixation probability. Many of the known results for networks of individuals carry over to meta-populations, in particular for regular networks or low symmetric migration probabilities. However, when patch sizes differ we find interesting deviations between structured meta-populations and networks of individuals. For example, a two patch structure with unequal population size suppresses selection for low migration probabilities.
Are experiment sample sizes adequate to detect biologically important interactions between multiple stressors?
Authors: Burgess Benjamin J. , Jackson Michelle C. , Murrell David J.
Published: July 2021

As most ecosystems are being challenged by multiple, co-occurring stressors, an important challenge is to understand and predict how stressors interact to affect biological responses. A popular approach is to design factorial experiments that measure biological responses to pairs of stressors and compare the observed response to a null model expectation. Unfortunately, we believe experiment sample sizes are inadequate to detect most non-null stressor interaction responses, greatly hindering progress. Determination of adequate sample size requires (i) knowledge of the detection ability of the inference method being used, and (ii) a consideration of the smallest biologically meaningful deviation from the null expectation. However, (i) has not been investigated and (ii) is yet to be discussed. Using both real and simulated data we show sample sizes typical of many experiments (<10) can only detect very large deviations from the additive null model, implying many important non-null stressor-pair interactions are being missed. We also highlight how only reporting statistically significant results at low samples sizes greatly overestimates the degree of non-additive stressor interactions. Computer code that simulates data under either additive or multiplicative null models is provided to estimate statistical power for user defined responses and sample sizes and we recommend this is used to aid experimental design and interpretation of results. We suspect that most experiments may require 20 or more replicates per treatment to have adequate power to detect non-additive. However, researchers still need to define the smallest interaction of interest, i.e. the lower limit for a biologically important interaction, which is likely to be system specific, meaning a general guide is unavailable. Sample sizes could potentially be increased by focussing on individual-level responses to multiple stressors, or by forming coordinated networks of researchers to repeat experiments in larger-scale studies. Our main analyses relate to the additive null model but we show similar problems occur for the multiplicative null model, and we encourage similar investigations into the statistical power of other null models and inference methods. Without knowledge of the detection abilities of the statistical tools at hand, or definition of the smallest meaningful interaction, we will undoubtedly continue to miss important ecosystem stressor interactions.
Shaping nanoparticle diffusion through biological barriers to drug delivery
Authors: Lee Benjamin J. , Cheema Yahya , Bader Shahed , Duncan Gregg A.
Published: July 2021

Nanoparticle drug delivery systems encounter many biological barriers, such as the extracellular matrix and mucus gels, that they must bypass to gain access to target cells. A design parameter that has recently gained attention is nanoparticle shape, as it has been shown elongated rod–shaped nanoparticles achieve higher diffusion rates through biological gels. However, the optimal dimensions of rod-shaped nanoparticles to enhance this effect has yet to be established. To systematically approach this, rod-shaped nanoparticles were synthesized by mechanically stretching 100 nm, 200 nm, and 500 nm spherical nanoparticles. Transmission electron microscopy confirmed this procedure yields a significant fraction of elongated rods and remaining spheres could be removed by centrifugation. Fluorescent microscopy and multiple particle tracking analysis was then used to characterize rod-shaped and spherical nanoparticle diffusion in MaxGel®, a model extracellular matrix hydrogel. When dispersed in MaxGel, we found rod-shaped nanoparticles exhibited the greatest enhancement in diffusion rate when their length far exceeds the average hydrogel network size. These results further establish the importance of shape as a design criterion to improve nanoparticle-based drug delivery systems.
The five Urochloa spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools
Authors: Higgins J , Tomaszewska P , Pellny TK , Castiblanco V , Arango J , Tohme J , Schwarzacher T , Mitchell RA , Heslop-Harrison JS , De Vega JJ
Published: July 2021

Background and Aims

Urochloa (syn. Brachiaria, and including some Panicum and Megathyrus) is a genus of tropical and subtropical grasses widely sown as forage to feed ruminants in the tropics. A better understanding of the diversity among Urochloa spp. allow us to leverage its varying ploidy levels and genome composition to accelerate its improvement, following the example from other crop genera.

Methods

We explored the genetic make-up and population structure in 111 accessions, which comprise the five Urochloa species used for the development of commercial cultivars. These accessions are conserved from wild materials from collection sites at their centre of origin in Africa. We used RNA-seq, averaging 40M reads per accession, to generate 1,167,542 stringently selected SNP markers that tentatively encompassed the complete Urochloa gene pool used in breeding.

Key Results

We identified ten subpopulations, which had no relation with geographical origin and represented ten independent gene pools, and two groups of admixed accessions. Our results support a division in U. decumbens by ploidy, with a diploid subpopulation closely related to U. ruziziensis, and a tetraploid subpopulation closely related to U. brizantha. We observed highly differentiated gene pools in U. brizantha, which were not related with origin or ploidy. Particularly, one U. brizantha subpopulation clustered distant from the other U. brizantha and U. decumbens subpopulations, so likely containing unexplored alleles. We also identified a well-supported subpopulation containing both polyploid U. decumbens and U. brizantha accessions; this was the only group containing more than one species and tentatively constitutes an independent “mixed” gene pool for both species. We observed two gene pools in U. humidicola. One subpopulation, “humidicola-2”, was much less common but likely includes the only known sexual accession in the species.

Conclusions

Our results offered a definitive picture of the available diversity in Urochloa to inform breeding and resolve questions raised by previous studies. It also allowed us identifying prospective founders to enrich the breeding gene pool and to develop genotyping and genotype-phenotype association mapping experiments.

HIGHLIGHT

We clarified the genetic make-up and population structure of 111 Urochloa spp. forage grasses to inform cultivar development.
Venous activation of MEK/ERK drives development of arteriovenous malformation and blood flow anomalies with loss of Rasa1
Authors: Greysson-Wong Jasper , Rode Rachael , Ryu Jae-Ryeon , Rinker Kristina D. , Childs Sarah J.
Published: July 2021

Vascular malformations develop when growth pathway signaling goes awry in the endothelial cells lining blood vessels. Arteriovenous malformations (AVMs) arise where arteries and veins abnormally connect in patients with loss of RASA1, a Ras GTPase activating protein, and, as we show here, in zebrafish rasa1 mutants. Mutant fish develop massively enlarged vessels at the connection between artery and vein in the tail vascular plexus. These AVMs progressively enlarge and become filled with slow-flowing blood and have a greater drop in pulsatility from the artery to the vein. Expression of the flow responsive transcription factor klf2a is diminished in rasa1 mutants, suggesting changes in flow velocity and pattern contribute to the progression of vessel malformations. Migration of endothelial cells is not affected in rasa1 mutants, nor is cell death or proliferation. Early developmental artery-vein patterning is also normal in rasa1 mutants, but we find that MEK/ERK signaling is ectopically activated in the vein as compared to high arterial activation seen in wildtype animals. MEK/ERK signaling inhibition prevents AVM development of rasa1 mutants, demonstrating venous MEK/ERK drives the initiation of rasa1 AVMs. Thus, rasa1 mutants show overactivation of MEK/ERK signaling causes AVM formation, altered blood flow and downstream flow responsive signaling.

The zebrafish model ofRASA1capillary malformation and arteriovenous malformation (CM-AVM1) develops cavernous vascular malformations driven by ectopic MEK/ERK signaling in the vein, disrupting flow and downstream mechanosensitive signaling.
SyMBac: Synthetic Micrographs for Accurate Segmentation of Bacterial Cells using Deep Neural Networks
Authors: Hardo Georgeos , Noka Maximilian , Bakshi Somenath
Published: July 2021

We present a novel method of bacterial image segmentation using machine learning models trained with Synthetic Micrographs of Bacteria (SyMBac). SyMBac is a tool that allows for rapid, automatic creation of arbitrary amounts of training data, combining detailed models of cell growth, physical interactions, and microscope optics to create synthetic images which closely resemble real micrographs. The major advantages of our approach are: 1) synthetic training data can be generated virtually instantly, and on demand; 2) these synthetic images are accompanied by perfect ground truth positions of cells, meaning no data curation is required; 3) different biological conditions, imaging platforms, and imaging modalities can be rapidly simulated, meaning any change in one’s experimental setup no longer requires the laborious process of manually generating new training data for each change. Our benchmarking results demonstrate that models trained on SyMBac data generate more accurate and precise cell masks than those trained on human annotated data, because the model learns the true position of the cell irrespective of imaging artefacts. Machine-learning models trained with SyMBac data are capable of analysing data from various imaging platforms and are robust to drastic changes in cell size and morphology.
Testing the accuracy of 3D automatic landmarking via genome-wide association studies
Authors: Savriama Yoland , Tautz Diethard
Published: July 2021

Background

Various advances in 3D automatic phenotyping and particularly in landmark-based geometric morphometric methods have been made, but only a few studies have tested the reliability of such automatic procedures in morphometric analyses. It is generally accepted that automatic landmarking compromises the capture of the actual biological variation, and this not only affects its performance to effectively detect differences among sample means but also the structure of covariance matrices. However, no studies have directly tested the actual impact of such landmarking approaches in analyses requiring a large number of specimens and for which the precision of phenotyping is crucial to capture an actual biological signal adequately.

Results

Here, we use a recently developed 3D atlas-based automatic landmarking method to test its accuracy in detecting QTLs associated with craniofacial development of the house mouse skull and lower jaws for a large number of specimens (circa 700) that were previously phenotyped via a semiautomatic landmarking method complemented with manual adjustment. We compare both landmarking methods with univariate and multivariate mapping of the skull and the lower jaws. In the univariate mapping, the automatic approach failed to recover the same SNPs and found only 1 out of 17 previously identified QTLs for the skull, but found one new QTL. Similarly, for the lower jaws, the automatic approach failed to recover the same SNPs but found 2 neighbouring SNPs for 1 out of 8 previously identified QTLs. For centroid size, the same general results were recovered by the automatic method for both the skull and lower jaws, with the same peak SNP being found for the lower jaws. In the multivariate mapping, the automatic approach did not detect the same markers nor QTLs having their regions overlapping with the ones identified with the semi-automatic procedure for the skull, while the same marker, which is also the peak SNP and sole QTL, was recovered by the automatic pipeline for lower jaws.

Conclusion

Our results confirm the notion that information is lost in the automated landmarking procedure but somewhat dependent on the analyzed structure. The automatic method seems to capture certain types of structures slightly better, such as lower jaws whose shape is almost entirely summarized by its outline and could be assimilated as a 2D flat object. By contrast, the more apparent 3D features exhibited by a structure such as the skull are not adequately captured by the automatic method. We conclude that using 3D atlas-based automatic landmarking methods requires careful consideration of the experimental question and the cautious interpretation of their results.
Developmental landscape of human forebrain at a single-cell level unveils early waves of oligodendrogenesis
Authors: van Bruggen David , Pohl Fabio , Langseth Christoffer Mattsson , Kukanja Petra , Lee Hower , Kabbe Mukund , Meijer Mandy , Hilscher Markus M. , Nilsson Mats , Sundström Erik , Castelo-Branco Gonçalo
Published: July 2021

Oligodendrogenesis in the human central nervous system has been mainly observed at the second trimester of gestation, a much later developmental stage compared to mouse. Here we characterize the transcriptomic neural diversity in the human forebrain at post conceptual weeks (PCW) 8 to 10, using single-cell RNA-Seq. We find evidence of the emergence of a first wave of oligodendrocyte lineage cells as early as PCW 8, which we also confirm at the epigenomic level with single-cell ATAC-Seq. Using regulatory network inference, we predict key transcriptional events leading to the specification of oligodendrocyte precursor cells (OPCs). Moreover, by profiling the spatial expression of fifty key genes using In Situ Sequencing (ISS), we identify regions in the human ventral fetal forebrain where oligodendrogenesis first occurs. Our results indicate evolutionary conservation of the first wave of oligodendrogenesis between mouse and human and describe regulatory mechanisms required for human OPC specification.
Single-cell atlas reveals meningeal leukocyte heterogeneity in the developing mouse brain
Authors: Zelco Aura , Börjesson Vanja , de Kanter Jurrian K. , Lebrero-Fernandez Cristina , Lauschke Volker M. , Rocha-Ferreira Eridan , Nilsson Gisela , Nair Syam , Svedin Pernilla , Bemark Mats , Hagberg Henrik , Mallard Carina , Holstege Frank C.P. , Wang Xiaoyang
Published: July 2021

The meninges are important for brain development and pathology. Using single-cell RNA sequencing, we have generated the first comprehensive transcriptional atlas of neonatal mouse meningeal leukocytes under normal conditions and after perinatal brain injury. We identified almost all known leukocyte subtypes and found differences between neonatal and adult border-associated macrophages, thus highlighting that neonatal border-associated macrophages are functionally immature with regards to immune responses compared with their adult counterparts. We also identified novel meningeal microglia-like cell populations that may participate in white matter development. Early after the hypoxic–ischemic insult, neutrophil numbers increased and they exhibited increased granulopoiesis, suggesting that the meninges are an important site of immune cell expansion with implications for the initiation of inflammatory cascades after neonatal brain injury. Our study provides a single-cell resolution view of the importance of meningeal leukocytes at the early stage of development in health and disease.
Nopp140-chaperoned 2′-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity
Authors: Bizarro Jonathan , Deryusheva Svetlana , Wacheul Ludivine , Gupta Varun , Ernst Felix G.M. , Lafontaine Denis L.J. , Gall Joseph G. , Meier U. Thomas
Published: July 2021

Spliceosomal small nuclear RNAs (snRNAs) are modified by small Cajal body (CB)-specific ribonucleoproteins (scaRNPs) to ensure snRNP biogenesis and pre-mRNA splicing. However, the function and subcellular site of snRNA modification are largely unknown. We show that CB localization of the protein Nopp140 is essential for concentration of scaRNPs in that nuclear condensate; and that phosphorylation by casein kinase 2 (CK2) at ∼80 serines targets Nopp140 to CBs. Transiting through CBs, snRNAs are apparently modified by scaRNPs. Indeed, Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2′-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Additionally, alternative splicing patterns change indicating that these modifications in U1, U2, U5, and U12 snRNAs safeguard splicing fidelity. Given the importance of CK2 in this pathway, compromised splicing could underlie the mode of action of small molecule CK2 inhibitors currently considered for therapy in cholangiocarcinoma, hematological malignancies, and COVID-19.
Genomic architecture constrained placental mammal X Chromosome evolution
Authors: Brashear Wesley A. , Bredemeyer Kevin R. , Murphy William J.
Published: July 2021

Susumu Ohno proposed that the gene content of the mammalian X Chromosome should remain highly conserved due to dosage compensation. X Chromosome linkage (gene order) conservation is widespread in placental mammals but does not fall within the scope of Ohno's prediction and may be an indirect result of selection on gene content or selection against rearrangements that might disrupt X-Chromosome inactivation (XCI). Previous comparisons between the human and mouse X Chromosome sequences have suggested that although single-copy X Chromosome genes are conserved between species, most ampliconic genes were independently acquired. To better understand the evolutionary and functional constraints on X-linked gene content and linkage conservation in placental mammals, we aligned a new, high-quality, long-read X Chromosome reference assembly from the domestic cat (incorporating 19.3 Mb of targeted BAC clone sequence) to the pig, human, and mouse assemblies. A comprehensive analysis of annotated X-linked orthologs in public databases demonstrated that the majority of ampliconic gene families were present on the ancestral placental X Chromosome. We generated a domestic cat Hi-C contact map from an F1 domestic cat/Asian leopard cat hybrid and demonstrated the formation of the bipartite structure found in primate and rodent inactivated X Chromosomes. Conservation of gene order and recombination patterns is attributable to strong selective constraints on three-dimensional genomic architecture necessary for superloop formation. Species with rearranged X Chromosomes retain the ancestral order and relative spacing of loci critical for superloop formation during XCI, with compensatory inversions evolving to maintain these long-range physical interactions.
Three-dimensional missense tolerance ratio analysis
Authors: Perszyk Riley E. , Kristensen Anders S. , Lyuboslavsky Polina , Traynelis Stephen F.
Published: July 2021

A wealth of genetic information is available describing single-nucleotide variants in the human population that appear to be well-tolerated and in and of themselves do not confer disease. These variant data sets contain signatures about the protein structure-function relationships and provide an unbiased view of various protein functions in the context of human health. This information can be used to determine regional intolerance to variation, defined as the missense tolerance ratio (MTR), which is an indicator of stretches of the polypeptide chain that can tolerate changes without compromising protein function in a manner that impacts human health. This approach circumvents the lack of comprehensive data by averaging the data from adjacent residues on the polypeptide chain. We reasoned that many motifs in proteins consist of nonadjacent residues, but together function as a unit. We therefore developed an approach to analyze nearest neighbors in three-dimensional space as determined by crystallography rather than on the polypeptide chain. We used members of the GRIN gene family that encode subunits of NMDA-type ionotropic glutamate receptors (iGluRs) to exemplify the differences between these methods. Our method, 3DMTR, provides new information about regions of intolerance within iGluRs, allows consideration of protein–protein interfaces in multimeric proteins, and moves this important research tool from one-dimensional analysis to a structurally relevant tool. We validate the improved 3DMTR score by showing that it more accurately classifies the functional consequences of a set of newly measured and published point mutations of Grin family genes than existing methods.
A new imaging technology based on Compton X-ray scattering
Authors: Saá Hernández Ángela , González-Díaz Diego , Villanueva Pablo , Azevedo Carlos , Seoane Marcos
Published: July 2021

A feasible implementation of a novel X-ray detector for highly energetic X-ray photons with a large solid angle coverage, optimal for the detection of Compton X-ray scattered photons, is described. The device consists of a 20 cm-thick sensitive volume filled with xenon at atmospheric pressure. When the Compton-scattered photons interact with the xenon, the released photoelectrons create clouds of secondary ionization, which are imaged using the electroluminescence produced in a custom-made multi-hole acrylic structure. Photon-by-photon counting can be achieved by processing the resulting image, taken in a continuous readout mode. Based on Geant4 simulations, by considering a realistic detector design and response, it is shown that photon rates up to at least 1011 photons s−1 on-sample (5 µm water-equivalent cell) can be processed, limited by the spatial diffusion of the photoelectrons in the gas. Illustratively, if making use of the Rose criterion and assuming the dose partitioning theorem, it is shown how such a detector would allow obtaining 3D images of 5 µm-size unstained cells in their native environment in about 24 h, with a resolution of 36 nm.