bluuebunny/crossref_metadata_2025 huggingface dataset:
Remdesivir (VEKLURY) for Treating COVID-19: Guinea Pig Ex Vivo and In Vivo Cardiac Electrophysiological Effects
Authors: Pilote Sylvie , Simard Chantale , Drolet Benoit
Published: July 2022

Bradycardia and QTc interval prolongation on the ECG have been reported with remdesivir (Veklury), an antiviral drug recently approved for treating severely ill patients with COVID-19. The objective was to evaluate the effects of remdesivir on cardiac electrophysiology ex vivo and in vivo. Ex vivo: Langendorff retroperfusion experiments were performed on isolated hearts from male Hartley guinea pigs (n = 23, total) exposed to either remdesivir 3, 10, or 30 µmol/L to assess drug-induced prolongation of the monophasic action potential duration measured at 90% repolarization (MAPD90). In vivo: ECG recordings using wireless cardiac telemetry were performed in guinea pigs (n = 6) treated with daily i.p. doses of remdesivir 5 mg/kg on day 1 and 2.5 mg/kg on days 2–10. Ex vivo remdesivir (3, 10, and 30 µmol/L) had no statistically significant effect on MAPD90, while pacing the hearts at basic stimulation cycle lengths of 200 or 250 milliseconds, or when the hearts were not paced and beating at their intrinsic heart rate. In a second set of similar ex vivo experiments, remdesivir 10 µmol/L did not potentiate the MAPD90-prolonging effects of dofetilide 20 nmol/L (n = 4) hearts. In vivo remdesivir caused small but statistically significant prolongations of the RR and QTcF intervals at day 1 (5 mg/kg) and at day 10 (2.5 mg/kg). No ventricular arrhythmias were ever observed under the effect of remdesivir. Remdesivir causes bradycardia, and mild QTc prolongation, which nonetheless, could be of clinical relevance in many hospitalized patients with COVID-19 concomitantly treated with multiple drugs.
Determining the Best Management Strategy for Preventing Short-Term Effects of Digital Display Use on Dry Eyes
Authors: Talens-Estarelles Cristian , García-Marqués José Vicente , Cerviño Alejandro , García-Lázaro Santiago
Published: July 2022

Objectives:

To assess and compare the effectiveness of four main management strategies for preventing short-term effects of digital display use on dry eye signs and symptoms.

Methods:

The ocular surface, tear film, and visual fatigue of 47 healthy individuals were assessed before and after reading on a laptop computer for 20 min under five different experimental conditions: control, instillation of artificial tears, taking a brief break, using a blue light screen filter, and blink control. Measurements included the Ocular Surface Disease Index (OSDI) Questionnaire, 5-item Dry Eye Questionnaire (DEQ-5), tear meniscus height (TMH), noninvasive keratograph break-up time (NIKBUT), bulbar conjunctival redness, and pupil size.

Results:

Worse results were obtained after the control and blue light filter conditions in all variables (P≤0.037). A higher post-task DEQ-5 score (P=0.013) and TMH (P<0.0005) were obtained when taking a brief break compared with pretask, although the increase in symptoms was significantly smaller than that observed in the nonmanagement control condition (P≤0.036). Similarly, a smaller increase in OSDI and DEQ-5 was obtained with the use of artificial tears and blink control in comparison with the control condition (P≤0.008), whereas a greater increase in DEQ-5 and decrease in NIKBUT was obtained for the blue light filter condition in comparison with the instillation of artificial tears (P=0.017) or blink control (P=0.008), respectively. Finally, a significantly lower post-task pupil size was obtained for all the conditions (P≤0.027).

Conclusions:

The instillation of artificial tears and blink control were the best management strategies for preventing short-term effects of digital display use on dry eyes. Conversely, using a blue light filter did not offer any benefits.
Investigation of SARS-CoV-2 in Postmortem Ocular Tissues and Evaluation of Its Effects on Corneal Donation
Authors: Korkmaz Hamide Ayben , Ceylan Ilkay , Ulutas Hafize Gokben
Published: July 2022

Purpose:

The purpose of this study was to investigate the presence of viruses in postmortem nasopharyngeal swabs and ocular tissues of patients with coronavirus disease 19 (COVID-19) confirmed through an antemortem reverse transcription polymerase chain reaction (RT-PCR) test.

Methods:

We recorded demographic data, comorbidities, treatments, and vaccination status of the patients diagnosed with COVID-19 and monitored in the intensive care unit. Nasopharyngeal swab samples were collected from the patients within 2 hours postmortem followed by swabs from both eyes, lower and upper conjunctival sacs, corneal epithelial layer, and samples from anterior chamber fluid. The geneMAP 2019-nCoV severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) detection kit was used to detect the samples showing the presence of SARS-CoV-2.

Results:

Among the 47 patients (mean age 74 years, range 39–92) included in the study, 29 were men and 18 were women. The nasopharyngeal swab samples of 21 patients were positive for the RT-PCR test for SARS-CoV-2, whereas at least one of the ocular tissue samples in 6 of those patients were positive for the RT-PCR test for SARS-CoV-2. However, all ocular swab samples were tested negative for SARS-CoV-2 in the 26 patients with negative nasopharyngeal swab samples. The mean duration from COVID-19 diagnosis to mortality was 10 days (range 2–27 days) in patients with positive postmortem nasopharyngeal swab samples for SARS-CoV-2, compared with an average of 21 days (1–80 days) in patients who tested negative. This difference was statistically significant (P = 0.01).

Conclusions:

Cadavers with negative postmortem nasopharyngeal swab samples for SARS-CoV-2 and those with the time from diagnosis to death of >3 weeks may be considered as candidates for corneal donation.
Is it time to personalise glucose targets during critical illness?
Authors: Plummer Mark P. , Hermanides Jeroen , Deane Adam M.
Published: July 2022

Purpose of review

Dysglycaemia complicates most critical care admissions and is associated with harm, yet glucose targets, particularly in those with preexisting diabetes, remain controversial. This review will summarise advances in the literature regarding personalised glucose targets in the critically ill.

Recent findings

Observational data suggest that the degree of chronic hyperglycaemia in critically ill patients with diabetes attenuates the relationship between mortality and several metrics of dysglycaemia, including blood glucose on admission, and mean blood glucose, glycaemic variability and hypoglycaemia in the intensive care unit. The interaction between acute and chronic hyperglycaemia has recently been quantified with novel metrics of relative glycaemia including the glycaemic gap and stress hyperglycaemia ratio. Small pilot studies provided preliminary data that higher blood glucose thresholds in critically ill patients with chronic hyperglycaemia may reduce complications of intravenous insulin therapy as assessed with biomakers. Although personalising glycaemic targets based on preexisting metabolic state is an appealing concept, the recently published CONTROLLING trial did not identify a mortality benefit with individualised glucose targets, and the effect of personalised glucose targets on patient-centred outcomes remains unknown.

There is inadequate data to support adoption of personalised glucose targets into care of critically ill patients. However, there is a strong rationale empowering future trials utilising such an approach for patients with chronic hyperglycaemia.
Investigation and Analysis of the Effect of Knowledge, Attitude, and Behavior of Gastrointestinal Endoscopy Nurses on Occupational Protection Against COVID-19
Authors: He Yan , Guo Xin-Yue , Chen Hong-Bo , Liu Guan-Yi , Wang Yi-Han , Zhang Yu-Qian , Lv Yang
Published: July 2022

The purpose of this study was to investigate the effects of knowledge, attitude, and behavior (KAB) of gastrointestinal endoscopy nurses on occupational protection against COVID-19. We analyzed the influencing factors on KAB to provide a reference for the training of nurses on occupational protection in endoscopic centers. A convenience sample of 400 endoscopy nurses from 26 provinces and cities in China was surveyed using a questionnaire to determine their KAB about occupational protection against COVID-19. Job title was an influencing factor of endoscopy nurses' attitude toward occupational protection against COVID-19. The type of hospital, whether nurses had received training on COVID-19, number of training courses received, and nurses' satisfaction with the workload in their endoscopic center were the influencing factors for occupational protective behavior. Study participants had good knowledge of occupational protection against COVID-19. Their overall attitude was positive, but their protective behavior needs further improvement. Feasible interventions to strengthen the occupational protective behavior of endoscopy nurses during the COVID-19 epidemic are suggested to improve the overall occupational protection level of endoscopy nurses.
Perceptions of Research Burden and Retention Among Participants in ADRC Cohorts
Authors: Gabel Matthew , Bollinger Rebecca M. , Knox Melissa , Coble Dean W. , Grill Joshua D. , Edwards Dorothy F. , Stark Susan L. , Lingler Jennifer H.
Published: July 2022

Objectives:

Alzheimer disease (AD) and related dementias clinical research is associated with significant participant burden. The Perceived Research Burden Assessment (PeRBA) measures participants’ perceptions of logistical, psychological, and physical burdens. The purpose of this study was to assess PeRBA’s psychometric properties, perceptual sources, and behavioral consequences with participants in a multisite study of participant retention in longitudinal cohort studies of Alzheimer disease and related dementias.

Design:

Multicenter mixed methods.

Setting:

In-person or phone.

Participants:

A total of 443 participants at 4 NIA-funded Alzheimer Disease Research Centers (ADRCs) were randomly selected and invited to participate if they were 45 years of age or more, enrolled in longitudinal studies, and had a Clinical Dementia Rating Scale global score ≤1.

Measurements:

Participants completed a 20-minute survey including the 21-item PeRBA about their research participation.

Results:

PeRBA demonstrated high-internal consistency and convergent validity. PeRBA scores correlated with expected perceptual factors. Higher PeRBA scores were associated with lower attendance and higher dropout rates.

Conclusions:

PeRBA can be used by researchers to identify participants who may feel overburdened and tailor approaches and strategies to support participants in longitudinal AD studies, maximizing participation, and reducing dropout. Making efforts to increase participants’ understanding of study procedures, and building and maintaining trust throughout the study, can contribute to reducing perceived burden and potentially increasing retention in longitudinal AD studies.
The physical and mental health consequences of social isolation and loneliness in the context of COVID-19
Authors: Pai Nagesh , Vella Shae-Leigh
Published: July 2022

Purpose of review

Social isolation and loneliness are known contributors to all-cause mortality as well as a range of physical and mental health conditions. Therefore, this article reviews current literature pertaining to the effects of social isolation and loneliness on physical and mental health during the current COVID-19 pandemic.

Recent findings

Social isolation and loneliness contribute to a myriad of physical and mental health conditions. Specifically social isolation and loneliness contribute to the development of cardiovascular disease, diabetes mellitus, and cancer. However, most research indicated that poor lifestyle factors explained most of the association. Social isolation and loneliness are also associated with cognitive problems including dementia, immune system problems, and mental health conditions. Further social isolation and loneliness also spur behavioral issues that significantly affect physical and mental health.

Evidence suggests that social isolation and loneliness have significant consequences on the physical and mental health of the individual and that the move toward ending all protections against COVID-19 has significant implications for the vulnerable. Further the similarities between the effects of social isolation and loneliness are compared to some of the conditions evident in long-COVID.
Antipsychotic treatment in elderly patients on polypharmacy with schizophrenia
Authors: Stuhec Matej
Published: July 2022

Purpose of review

Elderly patients with schizophrenia (SCH) are treated with antipsychotics and are often on different comedications, including polypharmacy (five or more medications). Evidence-based guidelines and randomized controlled trials do not include patients on polypharmacy, something that represents a ‘gap’ between evidence-based recommendations and clinical prescribing patterns. In this context, narrative reviews are needed to help clinicians in daily practice.

Recent findings

Antipsychotic treatment efficacies in meta-analyses are similar in the elderly with SCH compared with the general population (medium effect size). Long-term cohort studies show that antipsychotic treatment reduces overall mortality, hospitalizations, and cardiovascular death. These studies are limited because polypharmacy was not studied. The prevalence of antipsychotic use as potentially inappropriate medications was very high in nursing homes (25%). The prevalence of antipsychotic polypharmacy was 40%. Different strategies to manage these problems are available, including collaboration with clinical pharmacists, leading to reduced polypharmacy and better adherence to treatment guidelines.

Elderly patients with SCH on polypharmacy are less frequently studied, although they represent many patients with SCH. Different potentially inappropriate medication lists and collaboration with clinical pharmacists represent effective strategies for medication optimization. More studies are needed on this topic (e.g., prospective nonrandomized studies).
Evidence that gecko setae are coated with an ordered nanometre-thin lipid film
Authors: Rasmussen Mette H. , Holler Katinka Rønnow , Baio Joe E. , Jaye Cherno , Fischer Daniel A. , Gorb Stanislav N. , Weidner Tobias
Published: July 2022

The fascinating adhesion of gecko to virtually any material has been related to surface interactions of myriads of spatula at the tips of gecko feet. Surprisingly, the molecular details of the surface chemistry of gecko adhesion are still largely unknown. Lipids have been identified within gecko adhesive pads. However, the location of the lipids, the extent to which spatula are coated with lipids, and how the lipids are structured are still open questions. Lipids can modulate adhesion properties and surface hydrophobicity and may play an important role in adhesion. We have therefore studied the molecular structure of lipids at spatula surfaces using near-edge X-ray absorption fine structure imaging. We provide evidence that a nanometre-thin layer of lipids is present at the spatula surfaces of the tokay gecko (
Gekko gecko
) and that the lipids form ordered, densely packed layers. Such dense, thin lipid layers can effectively protect the spatula proteins from dehydration by forming a barrier against water evaporation. Lipids can also render surfaces hydrophobic and thereby support the gecko adhesive system by enhancement of hydrophobic–hydrophobic interactions with surfaces.
Macaques preferentially attend to intermediately surprising information
Authors: Wu Shengyi , Blanchard Tommy , Meschke Emily , Aslin Richard N. , Hayden Benjamin Y. , Kidd Celeste
Published: July 2022

Normative learning theories dictate that we should preferentially attend to informative sources, but only up to the point that our limited learning systems can process their content. Humans, including infants, show this predicted strategic deployment of attention. Here, we demonstrate that rhesus monkeys, much like humans, attend to events of moderate surprisingness over both more and less surprising events. They do this in the absence of any specific goal or contingent reward, indicating that the behavioural pattern is spontaneous. We suggest this U-shaped attentional preference represents an evolutionarily preserved strategy for guiding intelligent organisms toward material that is maximally useful for learning.
A model of metformin mitochondrial metabolism in metachromatic leukodystrophy: first description of human Schwann cells transfected with CRISPR-Cas9
Authors: Sanchez-Álvarez Nayibe Tatiana , Bautista-Niño Paula Katherine , Trejos-Suárez Juanita , Serrano-Díaz Norma Cecilia
Published: July 2022

Metachromatic leukodystrophy is a neurological lysosomal deposit disease that affects public health despite its low incidence in the population. Currently, few reports are available on pathophysiological events related to enzyme deficiencies and subsequent sulfatide accumulation. This research aims to examine the use of metformin as an alternative treatment to counteract these effects. This was evaluated in human Schwann cells (HSCs) transfected or non-transfected with CRISPR-Cas9, and later treated with sulfatides and metformin. This resulted in transfected HSCs showing a significant increase in cell reactive oxygen species (ROS) production when exposed to 100 µM sulfatides (
p
= 0.0007), compared to non-transfected HSCs. Sulfatides at concentrations of 10 to 100 µM affected mitochondrial bioenergetics in transfected HSCs. Moreover, these analyses showed that transfected cells showed a decrease in basal and maximal respiration rates after exposure to 100 µM sulfatide. However, maximal and normal mitochondrial respiratory capacity decreased in cells treated with both sulfatide and metformin. This study has provided valuable insights into bioenergetic and mitochondrial effects of sulfatides in HSCs for the first time. Treatment with metformin (500 µM) restored the metabolic activity of these cells and decreased ROS production.
Fine-grain population structure and transmission patterns of Mycobacterium tuberculosis in southern Mozambique, a high TB/HIV burden area
Authors: Saavedra Cervera Belén , López Mariana G. , Chiner-Oms Álvaro , García Ana María , Cancino-Muñoz Irving , Torres-Puente Manuela , Villamayor Luis , Madrazo-Moya Carlos , Mambuque Edson , Sequera Guillermo Victor , Respeito Durval , Blanco Silvia , Augusto Orvalho , López-Varela Elisa , García-Basteiro Alberto L. , Comas Iñaki
Published: July 2022

Genomic studies of the Mycobacterium tuberculosis complex (MTBC) might shed light on the dynamics of its transmission, especially in high-burden settings, where recent outbreaks are embedded in the complex natural history of the disease. To this end, we conducted a 1 year prospective surveillance-based study in Mozambique. We applied whole-genome sequencing (WGS) to 295 positive cultures. We fully characterized MTBC isolates by phylogenetics and dating evaluation, and carried out a molecular epidemiology analysis to investigate further associations with pre-defined transmission risk factors. The majority of strains (49.5%, 136/275) belonged to lineage (L) 4; 57.8 % of them (159/275) were in genomic transmission clusters (cut-off 5 SNPs), and a strikingly high proportion (45.5%) shared an identical genotype (0 SNP pairwise distance). We found two ‘likely endemic’ clades, comprising 67 strains, belonging to L1.2, which dated back to the late 19th century and were associated with recent spread among people living with human immunodeficiency virus (PLHIV). We describe for the first time the population structure of MTBC in our region, a high tuberculosis (TB)/HIV burden area. Clustering analysis revealed an unforeseen pattern of spread and high rates of progression to active TB, suggesting weaknesses in TB control activities. The long-term presence of local strains in Mozambique, which were responsible for large transmission among HIV/TB-coinfected patients, calls into question the role of HIV in TB transmission.
A new machine learning method for cancer mutation analysis
Authors: Habibi Mahnaz , Taheri Golnaz
Published: July 2022

It is complicated to identify cancer-causing mutations. The recurrence of a mutation in patients remains one of the most reliable features of mutation driver status. However, some mutations are more likely to happen than others for various reasons. Different sequencing analysis has revealed that cancer driver genes operate across complex pathways and networks, with mutations often arising in a mutually exclusive pattern. Genes with low-frequency mutations are understudied as cancer-related genes, especially in the context of networks. Here we propose a machine learning method to study the functionality of mutually exclusive genes in the networks derived from mutation associations, gene-gene interactions, and graph clustering. These networks have indicated critical biological components in the essential pathways, especially those mutated at low frequency. Studying the network and not just the impact of a single gene significantly increases the statistical power of clinical analysis. The proposed method identified important driver genes with different frequencies. We studied the function and the associated pathways in which the candidate driver genes participate. By introducing lower-frequency genes, we recognized less studied cancer-related pathways. We also proposed a novel clustering method to specify driver modules in each type of cancer. We evaluated each cluster with different criteria, including the terms of biological processes and the number of simultaneous mutations in each cancer. Materials and implementations are available at: https://github.com/MahnazHabibi/Mutation_Analysis
GMHI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling
Authors: Chang Daniel , Gupta Vinod K. , Hur Benjamin , Cunningham Kevin Y. , Sung Jaeyun
Published: July 2022

We recently introduced the Gut Microbiome Health Index (GMHI), a stool-based indicator for monitoring health given the state of one’s gut microbiome. GMHI depends on health-prevalent and health-scarce species determined and validated using a pooled dataset of 5,026 stool shotgun metagenomic samples from 43 independent studies. Encouragingly, GMHI has already been utilized in various studies focusing on identifying differences in the gut microbiome between cases and controls. However, current computational barriers and logistical issues prevent researchers from computing, interpreting, and contextualizing GMHI, thereby limiting its further widespread utilization. Herein, we introduce the GMHI-webtool, a user-friendly browser application that computes GMHI, health-prevalent/scarce species, α-diversities, and taxonomic distributions of the gut microbiome from stool samples. Users of our interactive online tool can visualize their results and compare side-by-side with those from our pooled reference dataset, as well as export data in .csv format and high-resolution figures.

Availability and implementation

GMHI-webtool is freely available here: https://gmhi-webtool.github.io/. Source code: https://github.com/danielchang2002/GMHI-webtool.
Signal peptide mimicry primes Sec61 for client-selective inhibition
Authors: Rehan Shahid , Tranter Dale , Sharp Phillip P. , Lowe Eric , Anderl Janet L. , Muchamuel Tony , Abrishami Vahid , Kuivanen Suvi , Wenzell Nicole , Jennings Andy , Kalyanaraman Chakrapani , Craven Gregory B. , Strandin Tomas , Javanainen Matti , Vapalahti Olli , Jacobson Matt , McMinn Dustin , Kirk Christopher J. , Huiskonen Juha T. , Taunton Jack , Paavilainen Ville O.
Published: July 2022

Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here, we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of proinflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryo-EM structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.
Eco-evolutionary drivers of avian migratory connectivity
Authors: Fattorini Niccolò , Costanzo Alessandra , Romano Andrea , Rubolini Diego , Baillie Stephen , Bairlein Franz , Spina Fernando , Ambrosini Roberto
Published: July 2022

Understanding how individuals redistribute after migration assists in the conservation and management of mobile species, yet the eco-evolutionary drivers of migratory connectivity remain unclear. Taking advantage of an exceptionally large (~150,000 individuals, 83 species) and more-than-a-century long dataset of bird ringing encounters, we investigated determinants of avian migratory connectivity on both short- and long-distance migrants. Most species exhibited significant connectivity likely due to the large intraspecific variability in migration strategies, which often led to the identification of distinct migratory populations. Migratory connectivity was strongly predicted by geography, especially migration distance, but it was evolutionary labile and weakly influenced by biological traits due to flexibility in migratory behaviour. By unravelling determinants of migratory connectivity we improve knowledge about the resilience of migrants to ecological perturbations. Also, our population-level analysis provides a critical tool to inform transboundary conservation and management strategies by explicitly considering the large intraspecific variability of avian migration.
Towards solving the conundrum of plasmid mobility: networks of functional dependencies shape plasmid transfer
Authors: Ares-Arroyo Manuel , Coluzzi Charles , Rocha Eduardo P.C.
Published: July 2022

Plasmids are key drivers of bacterial evolution by transferring genes between cells via conjugation. Yet, half of the plasmids lack all protein coding genes for this process. We searched to solve this conundrum by identifying conjugative origins of transfer over thousands of plasmids and chromosomes ofEscherichia coliandStaphylococcus aureus. We found that plasmids carrying these sequences are very abundant and have the highest densities of antimicrobial resistance genes. They are hyper-parasites that directly hijack conjugative or mobilizable elements, but not both. These functional dependencies explain the co-occurrence of each type of plasmid in cells and illuminate the evolutionary relationships between the elements. We characterized systematically the genetic traits of plasmids in relation to conjugation and alternative mechanisms of transfer, and can now propose a confident putative mechanism of transfer for ca. 90% of them. The few exceptions could be passively mobilized by other processes. We conclude there is no conundrum concerning plasmid mobility.
Receptor levels determine binding affinity of WNT-3A to Frizzled 7 in a colorectal cancer model
Authors: Grätz Lukas , Sajkowska-Kozielewicz Joanna J. , Wesslowski Janine , Petzold Katja , Davidson Gary , Schulte Gunnar , Kozielewicz Paweł
Published: July 2022

WNT binding to Frizzleds (FZD) is a crucial step that leads to the initiation of signalling cascades governing multiple processes during embryonic development, stem cell regulation and adult tissue homeostasis. Recent efforts have enabled us to shed light on WNT-FZD pharmacology in overexpressed HEK293 cell systems. However, it is important to assess ligand binding at endogenous receptor levels as there might be differential binding behaviour in a native environment. Here, we focus on one FZD paralogue: FZD7, and study its interactions with WNT-3A in a CRISPR-Cas9-edited SW480 colorectal cancer model. SW480 cells were CRISPR-Cas9-edited to insert a HiBiT-tag on the N-terminus of FZD7, preserving the native signal peptide. Subsequently, these cells were used to study eGFP-WNT-3A association to endogenous and overexpressed HiBiT-FZD7using NanoBiT/BRET to measure ligand binding and quantification of NanoBiT-emitted luminescence to assess receptor internalization. eGFP-WNT-3A bound to endogenous HiBiT-FZD7with significantly higherkonand with lowerKdthan to overexpressed receptors. Importantly, as the fluorescent probe is an agonist, experiments performed in cell lysates demonstrated that eGFP-WNT-3A/HiBiT-FZD7binding assessment is not altered by receptor internalization. In conclusion, binding affinities of eGFP-WNT-3A to HiBiT-FZD7decreased with increasing receptor concentrations suggesting that HiBiT-FZD7overexpression fails to recapitulate ligand binding behaviour in a (patho-)physiologically relevant context where endogenous receptor expression levels are lower.
Pollinator mosaics mirror floral trait divergence within and between species ofCastilleja
Authors: Wenzell Katherine E. , Skogen Krissa A. , Fant Jeremie B.
Published: July 2022

Pollinator interactions are important in the evolution of floral traits, given that pollinators can directly influence plant fitness and mating patterns through interactions with flowers. However, geographic variation in both plant traits and floral visitors across multiple populations is largely understudied, despite being ubiquitous. This study explores whether a geographic mosaic of ecological interactions underlies observed patterns of floral divergence 1) among species of theCastilleja purpureacomplex (C. purpurea, C. citrina, andC. lindheimeri) and the congenerC. sessiliflora, as well as 2) withinC. sessiliflora, across its wide geographic range. We sampled floral visitors and floral traits (morphology and color) at 23 populations across a 1900 km study area in 1-3 years, with reproductive fitness (fruit set) data for 18 of these populations.

We documented a wide diversity of pollinator functional groups visiting the four focal species, including bees, butterflies, hawkmoths, and hummingbirds. Visitor assemblages varied among species and across geography in the composition and diversity of floral visitors. We found relationships between floral traits and visitation by certain pollinator groups, which often aligned with syndrome-associated predictions. Additionally, we found evidence that visitation from pollinators predicted via syndromes was associated with increased reproductive fitness for two species: the red-floweredC. lindheimeriand hummingbird visitors, and the long-floral-tubedC. sessilifloraand hawkmoths.

Beyond these cases, we found that pollinator functional groups were not restricted to plant species, and instead pollinators were largely generalist in their foraging behavior, suggesting the likelihood for incomplete reproductive isolation and the potential for ongoing gene flow among plant species where their ranges overlap.

This study provides a large-scale exploration of how variation in pollinator assemblages across distributions may underlie floral trait divergence within and among recently diverged species, even when characterized by largely generalized modes of pollination. Our extensive sampling of 23 populations over multiple years across a large geographic area highlights the value of range-wide studies for characterizing patterns of divergence and speciation mediated by ecological interactions.
Seed reserve mobilization and seedling morphology in a bioassay for the detection of genetically modified soybean
Authors: Lopes Costa Francisco Cleilson , López Peña Samanda , Andrade Pereira Welison
Published: July 2022

Germination and initial seedling development are physiological processes that determine the establishment of crops. During heterotrophic growth, each seedling develops from the biomass of its seeds. Thus, verifying the potential of genotypes to mobilize reserves under stress has been important. The aim of this study was to investigate how glyphosate affects the mobilization of reserves and seedling morphology. Two tolerant and two herbicide-sensitive cultivars were submitted to germination, seedling length and reserve mobilization tests, including treatments with glyphosate solutions (0, 0.06 and 0.12 %). The hypocotyl / radicle ratio and the efficiency of conversion of reserves to seedlings were also verified. The data were submitted to analysis of variance and test of means. It was observed that the percentage of normal seedlings and length seedlings were affected due to the concentration of the herbicide in the treatments, being the consequences more pronounced for sensitive cultivars; the glyphosate-tolerant genotype and with the best physiological quality mobilized more reserves and was more efficient in converting biomass to seedlings; in morphology, the average length of the seedlings was reduced due to the herbicide, being the roots affected in such a way that they became smaller than the hypocotyls. The herbicide affects the morphology of the seedlings mainly the radicle, and the mobilization of the reserves discriminates the genotypes regarding tolerance to glyphosate.
Identification of a sensory neuron Cav2.3 inhibitor within a new superfamily of macro-conotoxins
Authors: Hackney Celeste M. , Salcedo Paula Flórez , Mueller Emilie , Koch Thomas Lund , Kjelgaard Lau D. , Watkins Maren , Zachariassen Linda Grønborg , Tuelund Pernille Sønderby , McArthur Jeffrey R. , Adams David J. , Kristensen Anders S. , Olivera Baldomero , Finol-Urdaneta Rocio K. , Safavi-Hemami Helena , Morth Jens Preben , Ellgaard Lars
Published: July 2022

Animal venom peptides represent valuable compounds for biomedical exploration. The venoms of marine cone snails constitute a particularly rich source of peptide toxins, known as conotoxins. Here, we identify the sequence of an unusually large conotoxin, Mu8.1, that defines a new class of conotoxins evolutionarily related to the well-known con-ikot-ikots and two additional conotoxin classes not previously described. The crystal structure of recombinant Mu8.1 displays a saposin-like fold and shows structural similarity with con-ikot-ikot. Functional studies demonstrate that Mu8.1 curtails calcium influx in defined classes of murine somatosensory dorsal root ganglion (DRG) neurons. When tested on a variety of voltage-gated ion channels, Mu8.1 preferentially inhibited the R-type (Cav2.3) calcium channel. Ca2+signals from Mu8.1-sensitive DRG neurons were also inhibited by SNX-482, a known spider peptide modulator of Cav2.3 and voltage-gated K+(Kv4) channels. Our findings highlight the potential of Mu8.1 as a molecular tool to identify and study neuronal subclasses expressing Cav2.3. Importantly, this multidisciplinary study demonstrates the feasibility of large, disulfide-rich venom-component investigation, an endeavor that will lead to the discovery of novel structures and functions in the previously underexplored group of macro-conotoxins.
Executed and imagined grasping movements can be decoded from lower dimensional representation of distributed non-motor brain areas
Authors: Ottenhoff Maarten C. , Verwoert Maxime , Goulis Sophocles , Colon Albert J. , Wagner Louis , Tousseyn Simon , van Dijk Johannes P. , Kubben Pieter L. , Herff Christian
Published: July 2022

Using brain activity directly as input for assistive tool control can circumvent muscular dysfunction and increase functional independence for physically impaired people. Most invasive motor decoding studies focus on decoding neural signals from the primary motor cortex, which provides a rich but superficial and spatially local signal. Initial non-primary motor cortex decoding endeavors have used distributed recordings to demonstrate decoding of motor activity by grouping electrodes in mesoscale brain regions. While these studies show that there is relevant and decodable movement related information outside the primary motor cortex, these methods are still exclusionary to other mesoscale areas, and do not capture the full informational content of the motor system. In this work, we recorded intracranial EEG of 8 epilepsy patients, including all electrode contacts except those contacts in or adjacent to the central sulcus. We show that executed and imagined movements can be decoded from non-motor areas; combining all non-motor contacts into a lower dimensional representation provides enough information for a Riemannian decoder to reach an area under the curve of 0.83 ± 0.11. Additionally, by training our decoder on executed and testing on imagined movements, we demonstrate that between these two conditions there exists shared distributed information in the beta frequency range. By combining relevant information from all areas into a lower dimensional representation, the decoder was able to achieve high decoding results without information from the primary motor cortex. This representation makes the decoder more robust to perturbations, signal non-stationarities and neural tissue degradation. Our results indicate to look beyond the motor cortex and open up the way towards more robust and more versatile brain-computer interfaces.
Monoallelically-expressed Noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression
Authors: Hao Qinyu , Liu Minxue , Daulatabad Swapna Vidhur , Gaffari Saba , Srivastava Rajneesh , Song You Jin , Bhaskar Shivang , Moitra Anurupa , Mangan Hazel , Tseng Elizabeth , Gilmore Rachel B. , Freier Susan M. , Chen Xin , Wang Chengliang , Huang Sui , Chamberlain Stormy , Jin Hong , Korlach Jonas , McStay Brian , Sinha Saurabh , Janga Sarath Chandra , Prasanth Supriya G. , Prasanth Kannanganattu V.
Published: July 2022

Out of the several hundred copies of rRNA genes that are arranged in the nucleolar organizing regions (NOR) of the five human acrocentric chromosomes, ∼50% remain transcriptionally inactive. NOR-associated sequences and epigenetic modifications contribute to differential expression of rRNAs. However, the mechanism(s), controlling the dosage of active versus inactive rRNA genes in mammals is yet to be determined. We have discovered a family of ncRNAs, SNULs (Single NUcleolus Localized RNA), which form constrained sub-nucleolar territories on individual NORs and influences rRNA expression. Individual members of the SNULs monoallelically associate with specific NOR-containing chromosome. SNULs share sequence similarity to pre-rRNA and localize in the sub-nucleolar compartment with pre-rRNA. Finally, SNULs control rRNA expression by influencing pre-rRNA sorting to the DFC compartment and pre-rRNA processing. Our study discovered a novel class of ncRNAs that by forming constrained nucleolar territories on individual NORs contribute to rRNA expression.
Integrating analog and digital modes of gene expression at Arabidopsis FLC
Authors: Antoniou-Kourounioti Rea L. , Meschichi Anis , Reeck Svenja , Berry Scott , Menon Govind , Zhao Yusheng , Fozard John A. , Holmes Terri L. , Wang Huamei , Hartley Matthew , Dean Caroline , Rosa Stefanie , Howard Martin
Published: July 2022

Quantitative gene regulation at the cell population-level can be achieved by two fundamentally different modes of regulation at individual gene copies. A “digital” mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an “analog” mode involves graded expression levels at each gene copy. At the Arabidopsis floral repressor FLOWERING LOCUS C (FLC), “digital” Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether FLC regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modelling, we find that FLC expression before cold is regulated by both analog and digital modes. We observe a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual FLC gene copies, before subsequent digital silencing, consistent with the copies switching OFF stochastically and heritably without cold. This switch leads to a slow reduction in FLC expression at the cell population-level. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.
Single-cell multi-omics enabled discovery of alkaloid biosynthetic pathway genes in the medical plant Catharanthus roseus
Authors: Li Chenxin , Wood Joshua C. , Vu Anh Hai , Hamilton John P. , Rodriguez Lopez Carlos Eduardo , Payne Richard M. E. , Serna Guerrero Delia Ayled , Yamamoto Kotaro , Vaillancourt Brieanne , Caputi Lorenzo , O’Connor Sarah E. , Buell C. Robin
Published: July 2022

Advances in omics technologies now permit generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells, and high-resolution determination of gene regulatory features including 3-dimensional chromatin interactions. Using a complementary, multi-omics approach, we interrogated the monoterpene indole alkaloid (MIA) biosynthetic pathway in Catharanthus roseus, a source of leading anti-cancer drugs. We identified not only new clusters of genes involved in MIA biosynthesis on the eight C. roseus chromosomes but also rampant gene duplication including paralogs of MIA pathway genes. Clustering was not limited to the linear genome and through chromatin interaction data, MIA pathway genes were shown to be present within the same topologically associated domain, permitting identification of a secologanin transporter. Single cell RNA-sequencing revealed exquisite and sequential cell-type specific partitioning of the leaf MIA biosynthetic pathway that, when coupled with a newly developed single cell metabolomics approach, permitted identification of a reductase that yields the bis-indole alkaloid anhydrovinblastine. Last, we revealed cell-type specific expression in the root MIA pathway that is conferred in part by neo- and sub-functionalization of paralogous MIA pathway genes. This study highlights how a suite of omic approaches, including single cell gene expression and metabolomics, can efficiently link sequence with function in complex, specialized metabolic pathways of plants.
Directed Differentiation of Human iPSCs to Functional Ovarian Granulosa-Like Cells via Transcription Factor Overexpression
Authors: Smela Merrick Pierson , Kramme Christian , Fortuna Patrick , Adams Jessica , Dong Edward , Kobayashi Mutsumi , Brixi Garyk , Tysinger Emma , Kohman Richie. E. , Shioda Toshi , Chatterjee Pranam , Church George M.
Published: July 2022

An in vitro model of human ovarian follicles would greatly benefit the study of female reproduction. Ovarian development requires the combination of germ cells and their supporting somatic cells, known as granulosa cells. Whereas efficient protocols exist for generating human primordial germ cell-like cells (hPGCLCs) from human iPSCs, a method of generating granulosa cells has been elusive. Here we report that simultaneous overexpression of two transcription factors (TFs) can direct the differentiation of human iPSCs to granulosa-like cells. We elucidate the regulatory effects of several granulosa-related TFs, and establish that overexpression of NR5A1 and either RUNX1 or RUNX2 is necessary and sufficient to generate granulosa-like cells. Our granulosa-like cells form ovary-like organoids (ovaroids) when aggregated with hPGCLCs, and recapitulate key ovarian phenotypes including support of germ cell maturation, follicle formation, and steroidogenesis. This model system will provide unique opportunities for studying human ovarian biology, and may enable the development of therapies for female reproductive health.
Effect of Charge Distribution on the Dynamics of Polyampholytic Disordered Proteins
Authors: Devarajan Dinesh Sundaravadivelu , Rekhi Shiv , Nikoubashman Arash , Kim Young C. , Howard Michael P. , Mittal Jeetain
Published: July 2022

The stability and physiological function of many biomolecular coacervates depend on the structure and dynamics of intrinsically disordered proteins (IDPs) that typically contain a significant fraction of charged residues. Although the effect of relative arrangement of charged residues on IDP conformation is a well-studied problem, the associated changes in dynamics are far less understood. In this work, we systematically interrogate the effects of charge distribution on the chain-level and segmental dynamics of polyampholytic IDPs in dilute solutions. We study a coarse-grained model polyampholyte consisting of an equal fraction of two oppositely charged residues (glutamic acid and lysine) that undergoes a transition from an ideal chain-like conformation for uniformly charge-patterned sequences to a semi-compact conformation for highly charge-segregated sequences. Changes in the chain-level dynamics with increasing charge segregation correlate with changes in conformation. The chain-level and segmental dynamics conform to simple homopolymer models for uniformly charge-patterned sequences but deviate with increasing charge segregation, both in the presence and absence of hydrodynamic interactions. We discuss the significance of these findings, obtained for a model polyampholyte, in the context of a charge-rich intrinsically disordered region of the naturally occurring protein LAF-1. Our findings have important implications for understanding the effects of charge patterning on the dynamics of polyampholytic IDPs in dilute conditions using polymer scaling theories.
Phylogenomic analysis of the Neocallimastigomycota: Proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae
Authors: Hanafy Radwa A. , Wang Yan , Stajich Jason E. , Pratt Carrie J. , Youssef Noha H. , Elshahed Mostafa H.
Published: July 2022

The anaerobic gut fungi (AGF) represent a coherent phylogenetic clade within the Mycota. Twenty genera have been described so far. Currently, the phylogenetic and evolutionary relationships between AGF genera remain poorly understood. Here, we utilized 53 transcriptomic datasets from 14 genera to resolve AGF inter-genus relationships using phylogenomics, and to provide a quantitative estimate (amino acid identity) for intermediate rank assignments. We identify four distinct supra-genus clades, encompassing genera producing polyflagellated zoospores, bulbous rhizoids, the broadly circumscribed genus Piromyces, and the Anaeromyces and affiliated genera. We also identify the genus Khoyollomyces as the earliest evolving AGF genus. Concordance between phylogenomic outputs and RPB1 and D/D2 LSU, but not RPB2, MCM7, or ITS1, phylogenies was observed. We combine phylogenomic analysis, and AAI outputs with informative phenotypic traits to propose accommodating 13/20 AGF genera into four families: Caecomycetaceae fam. nov. (encompassing genera Caecomyces and Cyllamyces), Piromycetaceae fam. nov. (encompassing the genus Piromyces), emend the description of fam. Neocallimastigaceae to only encompass genera Neocallimastix, Orpinomyces, Pecramyces, Feramyces, Ghazallomyces, and Aestipascuomyces, as well as the family Anaeromycetaceae to include the genera Oontomyces, Liebetanzomyces, and Capellomyces in addition to Anaeromyces. We refrain from proposing families for the deeply branching genus Khoyollomyces, and for genera with uncertain position (Buwchfawromyces, Joblinomyces, Tahromyces, Agriosomyces, Aklioshbomyces, and Paucimyces) pending availability of additional isolates and sequence data. Our results establish an evolutionary- grounded Linnaean taxonomic framework for the AGF, provide quantitative estimates for rank assignments, and demonstrate the utility of RPB1 as additional informative marker in Neocallimastigomycota taxonomy.