bluuebunny/crossref_metadata_2025 huggingface dataset:
An optimized workflow to generate and characterize iPSC-derived motor neuron (MN) spheroids
Authors: Castellanos-Montiel Maria Jose , Chaineau Mathilde , Franco-Flores Anna Kristyna , Haghi Ghazal , Carrillo-Valenzuela Dulce , Reintsch Wolfgang E. , Chen Carol X-Q , Durcan Thomas M.
Published: September 2022

Motor neuron diseases (MNDs) are characterized by the progressive degeneration of motor neurons (MNs) from the cortex, brainstem and/or the spinal cord. In an effort to understand the underlying causes of this selective degeneration, a multitude ofin vitromodels based on induced pluripotent stem cell (iPSC)-derived MNs have been developed. Moreover, different groups have started to use advanced 3D structures, composed of MNs and other cell types to increase the physiological relevance of suchin vitromodels. For instance, spheroids are simple 3D models that have the potential to be generated in large numbers that can be used across different assays. In this study, we generated MN spheroids and developed a workflow to analyze them. We confirmed the expression of different MN markers as the MN spheroids differentiate, at both the transcript and protein level, as well as their capacity to display functional activity in the form of action potentials (APs) and bursts. We also identified the presence of other cell types, namely interneurons and oligodendrocytes, which share the same neural progenitor pool with MNs. In summary, we successfully developed a MN 3D model, and we optimized a workflow that can be applied to their characterization and analysis. In the future, we will apply this model and workflow to the study of MNDs by generating MN spheroids from patient-derived iPSC lines, aiming to contribute to the development of more advance and physiologicalin vitrodisease models.
A novel sperm-derived seminal fluid protein inCaenorhabditisnematodes
Authors: Kasimatis Katja R. , Rehaluk Christine , Rowe Locke , Cutter Asher D.
Published: September 2022

Nematode sperm contain subcellular vesicles known as membranous organelles (MOs) that fuse with the cell membrane upon sperm activation to release their soluble contents into the extracellular space. The second most abundant proteins in the MOs belong to the conserved Nematode-Specific Peptide family, group F (NSPF) gene family. We hypothesize that these proteins contribute to seminal fluid and are part of post-insemination reproductive tract dynamics. We characterized the anatomical region where the NSPF proteins likely function during fertilization using whole-worm immunostaining of a His-taggednspf-1transgene. We confirmed that NSPF proteins are transferred to females during mating. NSPF proteins localize to the uterus lumen when transferred to mated females and in unmated adult hermaphrodites. These results suggest that the uterine localization of the NSPF proteins is likely a functional property of both male-derived sperm and self-sperm and not incidental to the point of transfer during mating. In males, we found that NSPF presence and abundance was correlated with reproductive maturity. We then used experimental evolution to compete the wildtype allele against a deletion allele in 10 replicate obligate-outcrossing populations. We calculated a mean selective disadvantage of 0.1% for the deletion allele, which indicated that the NSPF genes are beneficial to male fitness. This conclusion was reinforced by qualitative trends from lower powered single-generation fertility assays. Together we demonstrate that nematodes use a novel mechanism for generating seminal fluid proteins and show that the highly abundant NSPF proteins likely have a beneficial impact on fitness.
Diversification is correlated with temperature in white and sulfur butterflies
Authors: Carvalho Ana Paula S. , Owens Hannah L. , Laurent Ryan A. St , Earl Chandra , Dexter Kelly M. , Messcher Rebeccah L. , Willmott Keith R. , Aduse-Poku Kwaku , Collins Steve C. , Homziak Nicholas T. , Hoshizaki Sugihiko , Hsu Yu-Feng , Kizhakke Athulya G. , Kunte Krushnamegh , Martins Dino J. , Mega Nicolás O. , Morinaka Sadaharu , Peggie Djunijanti , Romanowski Helena P. , Sáfián Szabolcs , Vila Roger , Wang Houshuai , Braby Michael F. , Espeland Marianne , Breinholt Jesse W. , Pierce Naomi E. , Kawahara Akito Y. , Lohman David J.
Published: September 2022

Temperature is thought to be a key variable explaining global patterns of species richness. However, to investigate this relationship carefully, it is necessary to study clades with broad geographic ranges that are comprised of species inhabiting diverse biomes with well- characterized species ranges. In the present study, we investigate the link between temperature and diversification in the butterfly family Pieridae (sulfurs and whites) by combining Next Generation sequences and published molecular data with fine-grained distribution information. After building the most comprehensive phylogeny of the group, with almost 600 species and all higher taxa (subfamilies, tribes and subtribes), we found strong support for the following relationships within the family: Dismorphiinae + (Coliadinae + (Pseudopontiinae + Pierinae)). With a curated distribution dataset of over 800,000 occurrences, we conducted multiple comparative phylogenetic analyses that provided strong evidence that species in environments with more stable daily temperatures or with cooler maximum temperatures in the warm seasons have higher diversification rates. We also found a positive correlation between speciation and extinction with paleotemperature: as global temperature decreased through geological time, so did diversification rates. Although many studies demonstrate higher diversity in the tropics, we have been able to identify specific climate variables associated with changes in diversification, while also inferring the most robust and well sampled phylogenomic framework for Pieridae to date.
Luminal epithelial cells integrate variable responses to aging into stereotypical changes that underlie breast cancer susceptibility
Authors: Sayaman Rosalyn W. , Miyano Masaru , Senapati Parijat , Zirbes Arrianna , Shalabi Sundus , Todhunter Michael E. , Seewaldt Victoria , Neuhausen Susan L. , Stampfer Martha R. , Schones Dustin E. , LaBarge Mark A.
Published: September 2022

Effects from aging in single cells are unpredictable, whereas aging phenotypes at the organ- and tissue-levels tend to appear as stereotypical changes. The mammary epithelium is a bilayer of two major phenotypically and functionally distinct cell lineages, the luminal epithelial and myoepithelial cells. Mammary epithelia exhibit substantial stereotypical changes with age that merits attention because they are putative breast cancer-cells-of-origin. We hypothesize that effects from aging that impinge upon maintenance of lineage fidelity increases susceptibility to cancer initiation. We identified two models of age-dependent changes in gene expression, directional changes and increased variance, which contributed to genome-wide loss of lineage fidelity. Age-dependent variant responses were common to both lineages, whereas directional changes were almost exclusively detected in luminal epithelia and implicated downregulation of chromatin and genome organizers such asSATB1. Epithelial expression of gap junction proteinGJB6increased with age, and modulation ofGJB6expression in heterochronous co-cultures revealed that it provided a communication conduit from myoepithelial cells that drove directional change in luminal cells. Age-dependent luminal transcriptomes comprised a prominent signal detectable in bulk tissue during aging and transition into cancers. A machine learning classifier based on luminal-specific aging distinguished normal from cancer tissue and was predictive of breast cancer subtype. We speculate that luminal epithelia are the ultimate site of integration of the variant responses to aging in their surrounding tissue and that their emergent aging phenotype both endows cells with the ability to become cancer-cells-of-origin and embodies a biosensor that presages cancer susceptibility.
Parvalbumin Neurons and Cortical Coding of Dynamic Stimuli: A Network Model
Authors: Nocon Jian Carlo , Boyd Isaac Paul , Gritton Howard , Han Xue , Sen Kamal
Published: September 2022

Cortical circuits feature both excitatory and inhibitory cells that underlie the encoding of dynamic sensory stimuli, e.g., speech, music, odors, and natural scenes. While previous studies have shown that inhibition plays an important role in shaping the neural code, how excitatory and inhibitory cells coordinate to enhance encoding of temporally dynamic stimuli is not fully understood. Recent experimental recordings in mouse auditory cortex have shown that optogenetic suppression of parvalbumin neurons results in a decrease of neural discriminability of dynamic stimuli. Here, we present a multilayer model of a cortical circuit that mechanistically explains these results. The model is based on parvalbumin neurons which respond to both stimulus onsets and offsets, as observed experimentally, and incorporates characteristic shortterm synaptic plasticity profiles of excitatory and parvalbumin neurons. We reveal that by tuning the relative strengths of onset and offset inputs to parvalbumin neurons, the model generates different regimes of coding dominated by rapid firing rate modulations or spike timing. Moreover, the model replicates the experimentally observed reduction in neural discrimination performance during optogenetic suppression of parvalbumin neurons. These results suggest that distinct onset and offset inputs to parvalbumin neurons enhance cortical discriminability of dynamic stimuli by encoding distinct temporal features, enhancing temporal coding, and reducing cortical noise.

New & Noteworthy

Here we propose a model for the mechanisms that underlie neuron responses in the auditory cortex. This study focuses on single channel tuning of simple interactions between neurons. Using physiologically relevant parameters that underly parvalbumin and excitatory neurons, in the proposed artificial network, we show that we can recreate observed results in live studies.
Natural variation in host defense strategies impacts both host and pathogen fitness
Authors: Pfenning-Butterworth Alaina C. , Vetter Rachel E. , Hite Jessica L.
Published: September 2022

Animals ranging from mosquitoes to humans often vary their feeding behavior when infected or merely exposed to pathogens. For example, some individuals drastically reduce their food intake (‘illness-mediated anorexia’) while others increase food intake (‘hyperphagia’). While these so-called ‘sickness behaviors’ are well documented, their functional consequences remain poorly resolved.

Here, we examine links between natural genetic variation in susceptibility to infection, feeding behaviors, multiple traits of the host, and within-host pathogen production. Using a zooplankton host (Daphnia dentifera) and a fungal pathogen (Metschnikowia bicuspidata) as a case study, we show that genotypic and dose-dependent variation in feeding behaviors are associated with both resistance and tolerance mechanisms.

In one genotype, immune-mediated anorexia was associated with increased tolerance to infection; unlike other genotypes, these individuals did not upregulate phenoloxidase activity, but lived longer, had the highest overall fecundity, and produced higher pathogen loads, despite their reduced growth rates and resultant smaller body sizes. In these hosts, peak parasite load remained unchanged, suggesting a tolerance mechanism that offset fecundity costs.

In other genotypes, feeding behaviors followed either a flat or hump-shaped pattern with pathogen dose, exhibiting hyperphagia at intermediate doses and anorexia at higher doses. In these cases, anorexia functioned primarily in resistance.

Our results suggest that infection-mediated changes in host feeding behavior — which are traditionally interpreted as immunopathology — may in fact serve as crucial components of host defense strategies. Moreover, these phenomena vary across host genotypes, and were associated with apparent trade-offs with another melanization component of immune defense. Together, these results underscore that while resistance and tolerance are typically viewed as alternative and fixed defense strategies, the immense genetic diversity for immune defense may result in more of a plastic spectrum spanning a gradient from resistance to tolerance.
A natural language fMRI dataset for voxelwise encoding models
Authors: LeBel Amanda , Wagner Lauren , Jain Shailee , Adhikari-Desai Aneesh , Gupta Bhavin , Morgenthal Allyson , Tang Jerry , Xu Lixiang , Huth Alexander G.
Published: September 2022

Speech comprehension is a complex process that draws on humans’ abilities to extract lexical information, parse syntax, and form semantic understanding. These sub-processes have traditionally been studied using separate neuroimaging experiments that attempt to isolate specific effects of interest. More recently it has become possible to study all stages of language comprehension in a single neuroimaging experiment using narrative natural language stimuli. The resulting data are richly varied at every level, enabling analyses that can probe everything from spectral representations to high-level representations of semantic meaning. We provide a dataset containing BOLD fMRI responses recorded while 8 subjects each listened to 27 complete, natural, narrative stories (~6 hours). This dataset includes pre-processed and raw MRIs, as well as hand-constructed 3D cortical surfaces for each participant. To address the challenges of analyzing naturalistic data, this dataset is accompanied by a python library containing basic code for creating voxelwise encoding models. Altogether, this dataset provides a large and novel resource for understanding speech and language processing in the human brain.
Polylactide Degradation Activates Immune Cells by Metabolic Reprogramming
Authors: Maduka Chima V. , Alhaj Mohammed , Ural Evran , Habeeb Michael O. , Kuhnert Maxwell M. , Smith Kylie , Makela Ashley V. , Pope Hunter , Chen Shoue , Hix Jeremy M. , Mallett Christiane L. , Chung Seock-Jin , Hakun Maxwell , Tundo Anthony , Zinn Kurt R. , Hankenson Kurt D. , Goodman Stuart B. , Narayan Ramani , Contag Christopher H.
Published: September 2022

Polylactide (PLA) is the most widely utilized biopolymer in medicine. However, chronic inflammation and excessive fibrosis resulting from its degradation remain significant obstacles to extended clinical use. Immune cell activation has been correlated to the acidity of breakdown products, yet methods to neutralize the pH have not significantly reduced adverse responses. Using a bioenergetic model, we observed delayed cellular changes that were not apparent in the short-term. Amorphous and semi-crystalline PLA degradation products, including monomeric L-lactic acid, mechanistically remodel metabolism in cells leading to a reactive immune microenvironment characterized by elevated proinflammatory cytokines. Selective inhibition of metabolic reprogramming and altered bioenergetics both reduce these undesirable high cytokine levels and stimulate anti-inflammatory signals. Our results present a new biocompatibility paradigm by identifying metabolism as a target for immunomodulation to increase tolerance to biomaterials, ensuring safe clinical application of PLA-based implants for soft- and hard-tissue regeneration, and advancing nanomedicine and drug delivery.
Genome-wide ribosome profiling uncovers the role of iron in the control of protein translation
Authors: Barlit Hanna , Romero Antonia M. , Gülhan Ali , Patnaik Praveen K. , Tyshkovskiy Alexander , Martínez-Pastor María T. , Gladyshev Vadim N. , Puig Sergi , Labunskyy Vyacheslav M.
Published: September 2022

Iron is an essential trace element that serves as a cofactor for enzymes involved in multiple metabolic pathways, including ribosome biogenesis, protein translation, DNA synthesis and repair, lipid metabolism, and mitochondrial oxidative phosphorylation. In eukaryotes, iron deficiency leads to global inhibition of protein synthesis and coordinated changes in gene expression to limit iron utilization. Although several steps of protein translation depend on iron-containing enzymes, the contribution of iron to the translation process is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis as well as leads to translational repression of several groups of genes involved in iron-related processes. We further demonstrate that the RNA-binding proteins Cth1 and Cth2 play a central role in controlling the changes in protein translation by repressing the activity of the iron-dependent Rli1 ribosome recycling factor, inhibiting mitochondrial translation, and affecting the translation of genes involved in heme biosynthesis. We also discovered a mechanism, whereby iron deficiency represses translation ofMRS3mRNA, encoding mitochondrial iron transporter, through increased expression of antisense long non-coding RNA. Together, our results reveal complex gene expression and protein synthesis remodeling in response to low iron showing how this important metal affects protein translation at multiple levels.
DPAM: A Domain Parser for AlphaFold Models
Authors: Zhang Jing , Schaeffer R. Dustin , Durham Jesse , Cong Qian , Grishin Nick V.
Published: September 2022

The recent breakthroughs in structure prediction, where methods such as AlphaFold demonstrated near atomic accuracy, herald a paradigm shift in structure biology. The 200 million high-accuracy models released in the AlphaFold Database are expected to guide protein science in the coming decades. Partitioning these AlphaFold models into domains and subsequently assigning them to our evolutionary hierarchy provides an efficient way to gain functional insights of proteins. However, classifying such a large number of predicted structures challenges the infrastructure of current structure classifications, including our Evolutionary Classification of protein Domains (ECOD). Better computational tools are urgently needed to automatically parse and classify domains from AlphaFold models. Here we present a Domain Parser for AlphaFold Models (DPAM) that can automatically recognize globular domains from these models based on predicted aligned errors, inter-residue distances in 3D structures, and ECOD domains found by sequence (HHsuite) and structural (DALI) similarity searches. Based on a benchmark of 18,759 AlphaFold models, we demonstrated that DPAM could recognize 99.5% domains and assign correct boundaries for 85.2% of them, significantly outperforming structure-based domain parsers and homology-based domain assignment using ECOD domains found by HHsuite or DALI. Application of DPAM to the massive set of AlphaFold models will allow for more efficient classification of domains, providing evolutionary contexts and facilitating functional studies.
Neotropical birds and mammals show divergent behaviour responses to human pressure
Authors: Negret Pablo Jose , Luskin Mathew Scott , Gomez-Valencia Bibiana , Diaz-Pulido Angelica , Romero Luis Hernando , Restrepo Adriana , Zaehringer Julie G. , Ochoa-Quintero Jose Manuel , Mendes Calebe Pereira
Published: September 2022

Human presence and habitat disturbance (together ‘human pressure’ hereafter) can generate a deep fear in animals and this can influence their behaviour. Altered animal behaviour, such as shifts in diel activity patterns, affect many species and species interactions, which can induce changes in individual fitness, species-level population persistence, evolutionary dynamics, and ecosystem-level biodiversity. However, whether dial activity behavioural responses to human pressure are consistent among key functional groups has been poorly studied. For example, while medium to large mammal species tend to become more nocturnal in areas with high human pressure, it’s unclear if sympatric/co-occurring birds display similar or opposite patterns. This is an important knowledge gap because synchronous or opposing guild-level shifts can shape consequences for food-web dynamics (predation and competition), stability of interaction networks and ecosystem functioning. Here we used information from camera trapping along a gradient of human pressure in the Colombian Llanos region to assess diel activity changes in birds and mammals. We found that the diel activity of over 45% of the bird and 50% of the mammals assessed significantly changed where there was higher human pressures, with mammals becoming more nocturnal and birds more diurnal. The opposing behavioural responses to humans among vertebrate functional groups has significant repercussions for the fields of community ecology, including intraguild predation and competition, and may be a significant ecosystem-level conservation consideration.
Study on the mechanism of HE4 in hyperoxia-induced alveolar damage in rats
Authors: Yan Xiaofang , Feng Xing , Gao Yan , Liu Dawei , Bai Lin , Xu Lu
Published: September 2022

Objective

This study investigated the mechanism of human epididymis protein 4 (HE4) in hyperoxia-induced alveolar damage in rats.

Methods

The pathological changes of SD rat lung tissue were detected by hematoxylin-eosin staining. Plasma protein levels were measured by enzyme-linked immunosorbent assay (ELISA). The expression of mRNA was detected by real-time RT-PCR.

Results

Hyperoxia intervention within 7 days could induce acute lung injury in neonatal SD rats. Hyperoxia induction can increase HE4, MMP9 and TIMP1 in plasma and tissue of neonatal SD rats. By overexpressing and silencing HE4 gene in neonatal rat primary alveolar type II epithelial cells, we found that HE4 protein activates the phosphorylation of ERK and p65, activates the downstream MMP9 signaling pathway, inhibits MMP9 mRNA expression, inhibits protein activity, and reduces COLI degradation, increases collagen secretion, promoting matrix remodeling and fibrosis.

Conclusion

HE4 mediates the pathophysiological process of hyperoxia-induced lung injury in rats through ERK, MMP9 and TIMP1 signaling pathways. HE4 overexpression mediates lung basal remodeling and lung injury.
National trends in rates of undiagnosed HIV in key populations in Australia: a retrospective observational analysis from 2008 to 2019
Authors: Gray Richard T. , Camara Hawa , Khawar Laila , Grulich Andrew , Guy Rebecca , McGregor Skye , Medland Nicholas
Published: September 2022

Introduction

Determining the proportion of people living with HIV who are undiagnosed is critical for Australia to accurately assess the country’s progress toward UNAIDS’ 95-95-95 interim targets by 2025 and progress with elimination goals. We aimed to investigate the utility of two additional measures, the Yearly Diagnosed Fraction, and the Case Detection Rate, in elucidating trends over time in the rate of undiagnosed HIV.

Methods

Using routinely collected national HIV surveillance data, we produced estimates for the number living with undiagnosed HIV and the number of new HIV infections using the European Centre for Disease Protection and Control (ECDC) HIV modelling tool to calculate the Total Diagnosed Fraction (TDF), the Yearly Diagnosed Fraction (YDF), and the Case Detection Rate (CDR) from 2008 to 2019 for Australian-born and overseas-born individuals who have reported having male-to-male sexual contact, and heterosexual women and men. We calculated rate ratios using Poisson Regression models to compare trends for each sub-population.

Results

Over 2008-2019, each metric for the Australian-born male-to-male sexual contact group improved consistently over the period with the case detection rate rising above one in 2013. The total diagnosed fraction for the overseas born group fell slightly from 85.0% to 81.9%, the yearly diagnosed fraction fell from 23.1% to 17.8% and the case detection rate stayed below one, falling from 0.74 to 0.63. In the heterosexual group, women and men had consistent increasing trends for the total diagnosed fraction and yearly diagnosed fraction but with women having consistently higher estimates than men, 92.6% vs 80.8% and 26.3% vs 17.4%, respectively in 2019. However, heterosexual men had a declining case detection rate, falling below one in 2019 (0.83), compared to an increase for women.

Conclusion

The additional metrics presented provide important information on Australia’s progress toward HIV elimination. The more dynamic changes in the undiagnosed population seen highlight diverging trends for key populations with growing undiagnosed populations not seen in the total diagnosed fraction. Periodic trend analyses will help strengthen the use of the metrics and ease of interpretation for national surveillance reporting.
Natural ventilation, low CO2 and air filtration are associated with reduced indoor air respiratory pathogens
Authors: Raymenants Joren , Geenen Caspar , Budts Lore , Thibaut Jonathan , Thijssen Marijn , De Mulder Hannelore , Gorissen Sarah , Craessaerts Bastiaan , Laenen Lies , Beuselinck Kurt , Ombelet Sien , Keyaerts Els , André Emmanuel
Published: September 2022

Currently, the real-life impact of indoor climate, human behavior, ventilation and air filtration on respiratory pathogen detection and concentration are poorly understood. This hinders the interpretability of bioaerosol quantification in indoor air to surveil respiratory pathogens and transmission risk. We tested 341 indoor air samples from 21 community settings for 29 respiratory pathogens using qPCR. On average, 3.9 pathogens were positive per sample and 85.3% of samples tested positive for at least one. The number of detected pathogens and their respective concentrations varied significantly by pathogen, month, and age group in generalized linear (mixed) models and generalized estimating equations. High CO2 and low natural ventilation were independent risk factors for detection. CO2 concentration and air filtration were independently associated with their concentration. Occupancy, sampling time, mask wearing, vocalization, temperature, humidity and mechanical ventilation were not significant. Our results support the importance of ventilation and air filtration to reduce transmission.
Effects of exercise on sleep in children with overweight/obesity: A randomized clinical trial
Authors: Torres-Lopez Lucia V. , Migueles Jairo H. , Cadenas-Sanchez Cristina , Bendtsen Marcus , Henriksson Pontus , Mora-Gonzalez Jose , Löf Marie , Chaput Jean-Philippe , Ortega Francisco B.
Published: September 2022

Objectives

To examine 1) the chronic effects of a 20-week physical exercise program on device-assessed sleep and on sleep-disordered breathing (SDB); and 2) whether attending to a session of the exercise program had effects on device-assessed sleep the subsequent night in children with overweight/obesity.

Methods

A total of 99 children with overweight/obesity (n=47 in the exercise group) participated in this secondary analysis of the ActiveBrains randomized clinical trial. The exercise program included a combination of aerobic and resistance exercise training, 3-5 days/week (90 min/session). The control group was asked to maintain usual lifestyle. Sleep outcomes were measured using wrist actigraphy and included: total sleep time, total time in bed, sleep efficiency, and wake after sleep onset (WASO) time. SDB was assessed via the Paediatric Sleep Questionnaire.

Results

The ActiveBrains exercise program had a statistically significant effect on WASO time (−10.8 min/day, -0.5 standard deviations (SD), P=0.040). Furthermore, we observed a small non-statistically significant effect on sleep efficiency (+2%, 0.4 SD, P=0.1). No other chronic effects were observed on the other sleep outcomes. The nights (at maximum of 4) after attending the ActiveBrains exercise sessions, children showed higher total sleep time (+8 min, P=0.17), sleep efficiency (+1%, P=0.15), and lower WASO time (−6 min, P=0.18) although did not reach statistical significance.

Conclusion

A 20-week physical exercise program reduced WASO time in children with overweight/obesity in comparison with control group peers, yet we did not observe effects on SDB. Future randomized trials that include a clinical sample of children with poor sleep health at baseline are needed to better appreciate the role of exercise in sleep health.

Clinal Trial Registration

The ActiveBrains project is registered at ClinicalTrials.gov, no. NCT02295072. Data Sharing Statement: We did not obtain children’s parents consent to widely share the data nor was it included in the IRB protocol.

What’s known on this subject

Sleep is an essential component in children’s health. Previous researchers have found positive effects of exercise on sleep in adolescents with obesity, but the literature in childhood obesity is lacking.

What this study adds

A physical exercise program showed positive effects on device-assessed sleep habits in children with overweight/obesity, yet not on sleep-disordered breathing. Exercise programs should be promoted in children to improve their sleep health, especially in those with overweight/obesity.
Psychological safety, hierarchy, and other issues in operating room debriefing: reflexive thematic analysis of interviews from the frontline
Authors: McElroy Canice , Skegg Emma , Mudgway Mercedes , Murray Ngaire , Holmes Linda , Weller Jennifer , Hamill James
Published: September 2022

Background

Debriefing is a team discussion in a constructive, supportive environment. Barriers exist to consistent, effective, operative team debriefing.

Aim

To identify barriers to debriefing and their potential solutions as articulated by operating room personnel.

Design

Qualitative study.

Methods

Between December 2021 and February 2022 we interviewed operating room workers in a tertiary children’s hospital. We used purposive sampling to interview a variety of professions and specialties who work in the operating room environment. Interviews were audio-recorded, transcribed, and coded. The qualitative approach was reflexive thematic analysis with the theoretical framework was critical realism.

Results

Interviews were analysed from 40 operating room staff: 14 nurses,7 anaesthetic technicians, 7 anaesthetists, and 12 surgeons; 25 (62%) were female. The five key themes were: 1) “commitment to learning” – healthcare workers are committed to teamwork, quality improvement, and teamwork; 2) “it’s a safe space” – psychological safety is a pre-requisite for, and is enhanced by, debriefing; “natural born leader” – the value of leadership and also the limitations caused by psychological constructs about what and who is a leader; 4) “space-time” – finding time to debrief after routine operations and after critical events; and 5) “doing the basics well” – debriefing needs structure without being over-complicated.

Conclusion

Psychological safety is both a prerequisite for and a product of debriefing. Leadership, if viewed as a collective responsibility, could help break down power structures. Given the results of this study and evidence in the literature, it is likely that routine debriefing, if well done, will improve psychological safety, facilitate team learning, reduce errors, and improve patient safety.

Relevance to Clinical Practice

Debriefing is challenging to perform, requires leadership and training, but is worth the effort. Nurses can take a leading role in promoting routine debriefing in healthcare.

What does this paper contribute to the wider global clinical community?

Debriefing, if done well, promotes teamwork, psychological safety in the workplace, quality and safety, and organisational learning.

Setting up an effective debriefing programme is challenging but worth the effort.

Debriefing requires collaboration and nurses are well placed to be leaders in debriefing policy design and to lead multidisciplinary debriefs.
Fully Quantitative Measurements of Differential Antibody Binding to Spike Proteins from Wuhan, Alpha, Beta, Gamma, Delta and Omicron BA.1 variants of SARS-CoV-2: Antibody Immunity Endotypes
Authors: James-Pemberton Philip H. , Kohli Shivali , Twynham Jordan , Westlake Aaron C. , Antill Alex , Hunt Jade , Olkhov Rouslan V. , Shaw Andrew M.
Published: September 2022

A fully quantitative comparative analysis of the differential binding to spike variant proteins to SARS-CoV-2 has been performed for the variants: Wuhan (ancestral strain), Alpha, Beta, Gamma, Delta and Omicron BA.1. Evolution of immunity through five patient cohorts was studied including pre-pandemic, first infection, first vaccine, second vaccine and triple-vaccinated cohorts. A series of immunity endotypes has been observed: U(+) showing protection to all variants; single, double, triple, quadruple and quintuple dropout endotypes U(±); some with no variant protection other than Wuhan vaccine spike U(-); and some unclassified, U(∼). These endotypes may be imprinted. In the triple-vaccinated cohort (n = 54) there is a U(+) incidence of 65% (95% CI 51% - 76%) suggesting between half and three-quarters of the population have universal variant vaccine antibody protection; U(-) 6% (95% CI 2% - 15%) of the population have no variant antibody protection provided by the vaccine; and U(±)) with at least one dropout has a incidence of 20% (95% CI 12% - 33%). Extending the cohort incidence to the population, up to 76% of the population may have an imprinted immunity endotype to an epitope that is effective against all variants; critical for both protection and binding to the ACE2 receptor: a universal immunity endotype. However, up to 33% of the population may have an immunity endotype that will never produce an effective antibody response to SARS-CoV-2 unless the immunity imprint is broken.

Funding

Exeter University Alumni, Attomarker Ltd funded PhD studentship at the University of Exeter and Attomarker Ltd funding directly.
A rapid protocol for ribosome profiling of low input samples
Authors: Meindl Andreas , Romberger Markus , Lehmann Gerhard , Eichner Norbert , Kleemann Leon , Wu Jie , Danner Johannes , Boesl Maria , Mesitov Mikhail , Meister Gunter , König Julian , Leidel Sebastian , Medenbach Jan
Published: September 2022

Ribosome profiling provides quantitative, comprehensive, and high-resolution snapshots of cellular translation by the high-throughput sequencing of short mRNA fragments that are protected from nucleolytic digestion by ribosomes. While the overall principle is simple, the workflow of ribosome profiling experiments is complex and challenging, and typically requires large amounts of sample, limiting its broad applicability. Here, we present a new protocol for ultra-rapid ribosome profiling from low-input samples. It features a robust strategy for sequencing library preparation within one day that employs solid phase purification of reaction intermediates, allowing to reduce the input to as little as 0.1 pmol of RNA. Hence, it is particularly suited for the analyses of small samples or targeted ribosome profiling. Its high sensitivity and its ease of implementation will foster the generation of higher quality data from small samples, which opens new opportunities in applying ribosome profiling.
Optimization of arsB (Acr3) as a positive selection marker in the cyanobacterium Synechocystis sp. PCC 6803
Authors: Tejada Irene , Florencio Francisco J. , López-Maury Luis
Published: September 2022

The use of cyanobacteria as bio-factories for production of numerous compounds of interest (biofuels, bioplastics …) has attracted lots of attention mainly due to their simple nutritional requirements, coupled with the decrease in atmospheric CO2 levels. However, although cyanobacteria are easily genetically manipulated, there are few genetic tools developed and, in some cases, the modifications necessary for metabolic engineering are limited for this reason. We have developed a new positive selection marker based on the arsenic resistance system of the cyanobacterium Synechocystis sp. PCC 6803. In this cyanobacterium, resistance to arsenic is mediated by the arsBHC operon in which arsB encodes an arsenite transporter whose mutation confers hypersensitivity to the presence of both arsenite and arsenate. Using arsB mutant strain (SARSB) as recipient we introduced plasmids containing both arsB and an antibiotic resistance gene and transformants were selected using either arsenic or the antibiotic with similar efficiency. The plasmids and conditions to use the arsB gene as a selectable marker have been optimized. Furthermore, we have generated an integrative vector to delete the whole arsBHC operon that allows easy introduction of regulated genes in this locus. Analysis of this strain have shown that the ΔarsBHC mutant has a higher sensitivity to arsenite than the SARSB strain, even when they are complemented with an arsB copy. These suggest that arsH, arsC or both could have an additional role in arsenite resistance.
Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis
Authors: Härer Andreas , Rennison Diana J.
Published: September 2022

Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts’ ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism. We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we emphasize that the development and application of quantitative measures, such as multivariate vector analysis, should be further explored in microbiota research in order to better understand the role of microbiota dynamics during their hosts’ adaptive evolution, particularly in settings of parallel evolution.
Conformational changes linked to ADP release from human cardiac myosin bound to actin-tropomyosin
Authors: Doran M.H. , Rynkiewicz M.J. , Rassici D. , Bodt S.M.L. , Barry M. E. , Bullitt E. , Yengo C.M. , Moore J.R. , Lehman W.
Published: September 2022

Following binding to the thin filament, β-cardiac myosin couples ATP-hydrolysis to conformational rearrangements in the myosin motor that drive myofilament sliding and cardiac ventricular contraction. However, key features of the cardiac-specific actin-myosin interaction remain uncertain, including the structural effect of ADP release from myosin, which is ratelimiting during force generation. In fact, ADP release slows under experimental load or in the intact heart due to the afterload, thereby adjusting cardiac muscle power output to meet physiological demands. To further elucidate the structural basis of this fundamental process, we used a combination of cryo-EM reconstruction methodologies to determine structures of the human cardiac actin-myosin-tropomyosin filament complex at better than 3.4 Å-resolution in the presence and in the absence of Mg2+·ADP. Focused refinements of the myosin motor head and its essential light chains in these reconstructions reveal that small changes in the active site are coupled to significant rigid body movements of the myosin converter domain and a 16-degree lever arm swing. Our structures provide a mechanistic framework to understand the effect of ADP binding and release on human cardiac β-myosin and offer insights into the force-sensing mechanism displayed by the cardiac myosin motor.

Short Summary

Cryo-EM was used to elucidate high-resolution structures of actin-tropomyosin filaments decorated with human cardiac myosin in the rigor and ADP-bound states. Differences in the myosin lever arm orientation detected correlate with the overall actomyosin-linked force-sensitivity.
Nhlh1 and Nhlh2, a global transcriptional mechanism regulating commissural axon projection via Robo3 activation
Authors: Masuda Aki , Ajima Rieko , Saga Yumiko , Hirata Tatsumi , Zhu Yan
Published: September 2022

SUMMARY

Commissural neurons are highly heterogeneous in their developmental origins, neurotransmitter type and function, but all share the common feature of projecting axons across the midline. The floor plate-crossing commissural axons in mammals, from the spinal cord to the midbrain, are guided by a conserved molecular mechanism relying primarily on Netrin-1/DCC/Robo3 signaling. Up to date, we know very little about the upstream transcriptional program that specify commissural axon laterality, neither do we know if a common mechanism operates in all commissural neurons. Here, we identified a pair of highly related helix-loop-helix transcription factors, Nhlh1 and Nhlh2, as a global transcriptional mechanism that controls the laterality of all floor plate-crossing commissural axons. Forced expression of Nhlh1/2 induce ectopic Robo3 expression and contralateral axon projections. And mutant mice deficient in both genes show a remarkable reduction in Robo3 expression and a total lack of ventral commissures from the spinal cord to the midbrain. This global mechanism may interact with neuron type specific mechanism to achieve specific generation of commissural circuits.
Taurine as a key intermediate for host-symbiont interaction in the tropical spongeIanthella basta
Authors: Moeller Florian U. , Herbold Craig W. , Schintlmeister Arno , Mooshammer Maria , Motti Cherie , Behnam Faris , Watzka Margarete , Schweder Thomas , Albertsen Mads , Richter Andreas , Webster Nicole S. , Wagner Michael
Published: September 2022

Marine sponges are critical components of marine benthic fauna assemblages where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont ‘CandidatusTaurinisymbion ianthellae’ residing in the marine sponge,Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. ‘CandidatusTaurinisymbion ianthellae’ incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont ‘CandidatusNitrosospongia ianthellae’. Metaproteogenomic analyses also indicate that ‘CandidatusTaurinisymbion ianthellae’ likely imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay betweenIanthella bastaand its microbial symbionts.
Cd-induced cytosolic proteome changes in the cyanobacterium Anabaena sp. PCC7120 are mediated by LexA as one of the regulatory proteins
Authors: Srivastava Akanksha , Kumar Arvind , Biswas Subhankar , Srivastava Vaibhav , Rajaram Hema , Mishra Yogesh
Published: September 2022

LexA, a well-characterized transcriptional repressor of the SOS genes in heterotrophic bacteria, has been shown to regulate diverse genes in cyanobacteria. An earlier study showed that LexA overexpression in a cyanobacterium, Anabaena sp. PCC7120 reduces its tolerance to Cd stress. This was later shown to be due to modulation of photosynthetic redox poising by LexA under Cd stress. However, in light of the global regulatory nature of LexA and the prior prediction of AnLexA-box in a few heavy metal-responsive genes, we speculated that LexA has a broad role in Cd stress tolerance, with regulation over a variety of Cd stress-responsive genes in addition to the regulation on genes related with photosynthetic redox poising. Thus, to further expand the knowledge on the regulatory role of LexA in Cd stress tolerance, a cytosolic proteome profiling of Anabaena constitutively overexpressing LexA upon Cd stress was performed. The proteomic study revealed 25 differentially accumulated proteins (DAPs) in response to the combined effect of LexA overexpression and Cd stress, and the other 11 DAPs exclusively in response to either LexA overexpression or Cd stress. The 36 identified proteins were related with a variety of functions, including photosynthesis, carbon metabolism, antioxidative defence, protein turnover, chaperones, post-transcriptional modifications, and a few unknown and hypothetical proteins. The regulation of LexA on corresponding genes, as well as six previously reported Cd efflux transporters, was further validated by the presence of AnLexA-boxes, transcript, and/or promoter analyses. In a nutshell, this study identifies the regulation of LexA on several genes and proteins of various functional categories in Anabaena that are responsive to Cd stress, hence expanding the regulatory role of LexA under Cd stress.

Highlights

LexA overexpression was earlier shown to decrease Cd stress tolerance in Anabaena.

We examined the combined effect of LexA overexpression and Cd on Anabaena proteome.

Upon LexA overexpression or Cd stress or both, 36 differential proteins were found.

In silico, transcript and EMSA proved LexA regulation on them and few transporters.

The findings of this study extended the regulatory role of LexA in Cd tolerance.