bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing online support groups with psychoeducation versus psychoeducation alone for distressed breast cancer survivors: a randomized controlled trial
Authors: Baydoun Mohamad , Speca Michael , Taylor-Brown Jill , Stephen Joanne , Piedalue Katherine-Ann , Turner Jill , Carlson Linda E.
Published: July 2021

Background:

Online support groups are one forum that can help breast cancer survivors cope with negative mood states, but little is known about their effects compared to self-administered psycho-educational interventions. This randomized controlled trial compared the effects of synchronous, text-based professionally led online support groups (OSGs) plus a psychoeducational coping skills training program, called Nucare, versus Nucare alone in distressed survivors of breast cancer.

Methods:

Consented participants were randomized to an OSG (90-minute once-weekly session for 12 weeks) plus home-based Nucare or a self-directed home-based Nucare intervention alone. The primary outcome was the Profile of Mood States-Short Form – Total Mood Disturbance score (POMS-TMD). Secondary outcomes included measures of anxiety, depression, coping, illness intrusiveness, and loneliness. Outcomes were measured before and after the intervention, and 3 months post-intervention (follow-up).

Results:

One hundred twenty-five stage I–III breast cancer survivors enrolled with a mean age of 53 years (OSG plus Nucare [n = 68]; Nucare alone [n = 57]). There was a significant improvement in POMS-TMD scores among the entire study sample during the intervention period (Cohen's d 
= 
0.25, P 
= 
.002), which was maintained over follow-up. The group × time interactions on POMS-TMD over the intervention and follow-up periods were not significant (all Ps > .05), indicating neither group outperformed the other. Group x time interactions on three coping domains (positive reframing, use of instrumental support, self-blame) favored Nucare alone over OSG plus Nucare during the intervention period (Cohen's d ranged from 0.40 to 0.48), while group x time interactions over the follow-up period favored OSG plus Nucare over Nucare alone on loneliness (Cohen's d 
= 
0.34) and one coping domain (self-blame) (Cohen's d 
= 
0.58). Anxiety, depression, and illness intrusiveness were not significantly different between groups at any time point (all Ps 
> 
.05).

Conclusion:

OSGs plus Nucare were not found superior to Nucare alone in improving mood disturbance. Mood improvement among the entire sample indicates that regular use of either Nucare alone or in combination with OSGs may have the potential to ameliorate negative mood states in breast cancer survivors.
Does undertaking genome sequencing prompt actual and planned lifestyle-related behavior change in cancer patients and survivors? A qualitative study
Authors: Vatter Sabina , Bartley Nicci , Best Megan , Juraskova Ilona , Jacobs Chris , Ballinger Mandy L. , Thomas David M. , Butow Phyllis
Published: July 2021

Background:

In order for genomic testing to fulfil its promise of helping cancer patients and survivors to prevent future disease, it is important to consider its behavioral impact and outcomes. This study explored the factors that participants perceived would impact lifestyle-related behavioral intentions following genome sequencing (GS).

Methods:

Individual semistructured interviews were conducted to explore behavioral intentions with a purposive subsample of 24 adults with a past or current cancer of likely heritable aetiology who undertook germline GS as part of a larger genetic study (RisC). Participants were interviewed 12 months following their consent to a longitudinal psychosocial sub-study of RisC (PiGeOn study), before receipt of results. Data were analyzed using thematic analysis.

Results:

Analysis revealed 3 main themes: past prompts, barriers, and motivators to behavior change. The primary goal for behavioral change was to be healthy for oneself and one's family. Past experience of cancer facilitated positive modifications to lifestyle, such as increased exercise and healthy diet, higher prioritization of mental health and well-being, and regular health check-ups and tests. Maintaining these changes, however, was difficult for some due to daily commitments and lack of self-control. Limited knowledge and perceived inevitability of developing cancer due to genetic predisposition were recognized as barriers to making lifestyle changes. Concurrently, future receipt of actionable results was perceived as a powerful driver of behavior change.

Conclusion:

Understanding barriers and facilitators to behavior intention and patients’ attitudes to recommended lifestyle change in the context of genomic testing can be useful for health care professionals, to guide their discussions of behavioral change.
The Role of Alpha-1-Acid Glycoprotein in the Diagnosis and Treatment of Crush Syndrome-Induced Acute Kidney Injury
Authors: Lv Qi , Long Manman , Wang Xin , Shi Jie , Wang Pengtao , Guo Xiaoqin , Song Jie , Midgley Adam C. , Fan Haojun , Hou Shike
Published: July 2021

Background:

Crush syndrome (CS) is the most common cause of deaths following earthquakes and other disasters. The pathogenesis of CS has yet to be fully elucidated. Thus, clinical choice of ideal drug treatments for CS remains deficient.

Methods and Results:

In this study, we first evaluated the relation between extrusion force and the severities of CS. Rats were exposed to different extrusion forces: 1 kg, 3 kg, 5 kg, and 8 kg, respectively. Survival rates, crushed muscle tissue edema, serum biochemical parameters, and histopathological staining were used to assess severity. Our results showed that there were no statistical differences in survival rate or changes in thigh circumference among the different extrusion forces groups. However, serum levels of potassium, creatine kinase, blood urea nitrogen, creatinine, and myoglobin were elevated at 12- and 24-h post-decompression in 5 kg and 8 kg groups, compared with 1 kg and 3 kg groups. Histopathological staining demonstrated that the degree of organ damage to kidney, muscle, and lung tissues correlated with increasing extrusion force. We next analyzed changes in serum protein profiles in 3 kg or 5 kg extrusion pressure groups. A total of 76 proteins (20 upregulated, 56 downregulated) were found to be altered at all three time points (0, 12, and 72 h) post-decompression, compared with the control group. Three common upregulated proteins alpha-1-acid glycoprotein (α1-AGP), neutrophil gelatinase-associated lipocalin (NGAL), and Haptoglobin were selected for validation of increased expression. α1-AGP was explored as a treatment for CS-induced acute kidney injury (AKI). Intraperitoneal injection of α1-AGP protected kidneys from CS-induced AKI by regulating TNF-α and IL-6 production, attenuating neutrophil recruitment, and reducing renal cell apoptosis.

Conclusion:

Our findings demonstrated that the severity of crush injury is causally related to extrusion pressure and increase in blood serum markers. Our identification of the biomarker and treatment candidate, α1-AGP, suggests its implication in predicting the severity of CS and its use as a mediator of CS-induced AKI, respectively.
Genomic signatures of rapid adaptive divergence in a tropical montane species
Authors: Ericson Per G. P. , Irestedt Martin , She Huishang , Qu Yanhua
Published: July 2021

Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird (
Amblyornis papuensis
). Our results show that the two populations inhabiting the eastern and western Central Range became isolated
ca
11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.
Can we clinically identify pre-symptomatic and asymptomatic COVID-19?
Authors: Elhamamsy Salaheldin , DeVone Frank , Bayer Tom , Halladay Chris , Cadieux Marilyne , McConeghy Kevin , Rajan Ashna , Sachar Moniyka , Mujahid Nadia , Nanda Aman , McNicoll Lynn , Rudolph James L , Gravenstein Stefan
Published: July 2021

Objectives

COVID-19 has had a severe impact on morbidity and mortality among nursing home (NH) residents. Earlier detection of SARS-CoV-2 may position us to better mitigate risk of spread. Both asymptomatic or pre-symptomatic transmission are common in outbreaks, and threshold temperatures, such as 38C, for screening for infection could miss timely detection in the majority.

Design

Retrospective cohort study using electronic health records

Methods

We hypothesized that in long-term care residents, temperature trends with SARS-CoV-2 infection could identify infection in pre-symptomatic and asymptomatic individuals earlier. We collected information about age and other demographics, baseline temperature, and specific comorbidities. We created standardized definitions, and an alternative hypothetical model to test measures of temperature variation and compare outcomes to the VA reality.

Settings and participants

Our subjects were 6,176 residents of the VA NHs who underwent SARS-CoV-2 trigger testing.

Results

We showed that a change from baseline of >0.4C identifies 47% of the SARS-CoV-2 positive NH residents early, and achieves earlier detection by 42.2 hours. Range improves early detection to 55% when paired with a 37.2C cutoff, and achieves earlier detection by 44.4 hours. Temperature elevation >0.4C from baseline, when combined with a 0.7C range, would detect 52% early, leading to earlier detection by more than 3 days in 22% of the residents. This earlier detection comes at the expense of triggering 57,793 tests, as compared to the number of trigger tests ordered in the VA system of 40,691.

Conclusion and implications

Our model suggests that current clinical screening for SARS-CoV-2 in NHs can be substantially improved upon by triggering testing using a patient-derived baseline temperature with a 0.4C degree relative elevation or temperature variability of 0.7C trigger threshold for SARS-CoV2 testing. Such triggers could be automated in facilities that track temperatures in their electronic records.
Risk of Myocarditis from COVID-19 Infection in People Under Age 20: A Population-Based Analysis
Authors: Singer Mendel E. , Taub Ira B. , Kaelber David C
Published: July 2021

Background

There have been recent reports of myocarditis (including myocarditis, pericarditis or myopericarditis) as a side-effect of mRNA-based COVID-19 vaccines, particularly in young males. Less information is available regarding the risk of myocarditis from COVID-19 infection itself. Such data would be helpful in developing a complete risk-benefit analysis for this population.

Methods

A de-identified, limited data set was created from the TriNetX Research Network, aggregating electronic health records from 48 mostly large U.S. Healthcare Organizations (HCOs). Inclusion criteria were a first COVID-19 diagnosis during the April 1, 2020 - March 31, 2021 time period, with an outpatient visit 1 month to 2 years before, and another 6 months to 2 years before that. Analysis was stratified by sex and age (12-17, 12-15, 16-19). Patients were excluded for any prior cardiovascular condition. Primary outcome was an encounter diagnosis of myocarditis within 90 days following the index date. Rates of COVID-19 cases and myocarditis not identified in the system were estimated and the results adjusted accordingly. Wilson score intervals were used for 95% confidence intervals due to the very low probability outcome.

Results

For the 12-17-year-old male cohort, 6/6,846 (0.09%) patients developed myocarditis overall, with an adjusted rate per million of 450 cases (Wilson score interval 206 - 982). For the 12-15 and 16-19 male age groups, the adjusted rates per million were 601 (257 - 1,406) and 561 (240 - 1,313).

For 12-17-year-old females, there were 3 (0.04%) cases of myocarditis of 7,361 patients. The adjusted rate was 213 (73 - 627) per million cases. For the 12-15- and 16-19-year-old female cohorts the adjusted rates per million cases were 235 (64 - 857) and 708 (359 - 1,397).

The outcomes occurred either within 5 days (40.0%) or from 19-82 days (60.0%).

Conclusions

Myocarditis (or pericarditis or myopericarditis) from primary COVID19 infection occurred at a rate as high as 450 per million in young males. Young males infected with the virus are up 6 times more likely to develop myocarditis as those who have received the vaccine.
A significant increase in Tuberculosis diagnosis is required to mitigate the impact of COVID-19 on its future burden
Authors: Tovar Mario , Aleta Alberto , Sanz Joaquín , Moreno Yamir
Published: July 2021

The ongoing COVID-19 pandemic has greatly disrupted our everyday life, forcing the adoption of non-pharmaceutical interventions in many countries worldwide and putting public health services and healthcare systems worldwide under stress. These circumstances are leading to unintended effects such as the increase in the burden of other diseases. Here, using a data-driven epidemiological model for Tuberculosis (TB) spreading, we describe the expected rise in TB incidence and mortality that can be attributable to the impact of COVID-19 on TB surveillance and treatment in four high-burden countries. Our calculations show that the reduction in diagnosis of new TB cases due to the COVID-19 pandemic could result in 824250 (CI 702416-940873) excess deaths in India, 288064 (CI 245932-343311) in Indonesia, 145872 (CI 120734-171542) in Pakistan, and 37603 (CI 27852-52411) in Kenya. Furthermore, we show that it is possible to revert such unflattering TB burden scenarios by increasing the pre-covid diagnosis capabilities at least a 75% during 2 to 4 years. This would prevent almost all TB-related excess mortality caused by the COVID-19 pandemic, which will be observed if nothing is done to prevent it. Our work therefore provides guidelines for mitigating the impact of COVID-19 on tuberculosis epidemic in the years to come.
MicroRNA childhood Cancer Catalog (M3Cs): A Resource for Translational Bioinformatics Toward Health Informatics in Pediatric Cancer
Authors: Rashed Wafaa M. , Adel Fatima , Rezk Mohamed A. , Basiouny Lina , Rezk Ahmed A. , Abdel-Razek Ahmed H.
Published: July 2021

Background

MicroRNA childhood Cancer Catalog (M3Cs) is high-quality curated collection of published miRNA research studies on 16 pediatric cancer diseases. M3Cs scope was based on two approaches: data-driven clinical significance and data-driven human pediatric cell line models.

Method

M3Cs development passed through three phases: 1. Literature Mining: It includes external database search and screening. 2. Data processing that includes 3 steps: a-Data Extraction, b-Data Curation & annotation, c-Web Development. 3. Publishing: Shinyapps.io was used as a web interface for the deployment of M3Cs. M3Cs is now available online and can be accessed through https://m3cs.shinyapps.io/M3Cs/.

Results

For Data-driven clinical significance Approach, 538 miRNAs from 268 publications were reported in the clinical domain while 7 miRNAs from 5 publications were reported in the clinical & drug domain. For data-driven human pediatric cell line models approach, 538 miRNAs from 1268 publications were reported in cell line domain while 211 miRNAs from 177 publications in cell line & drug domain.

Conclusion

M3Cs acted to fill the gap by applying translational bioinformatics (TBI) general pathway to transfer data-driven research toward data-driven clinical care and/or hypothesis generation. Aggregated and well-curated data of M3Cs will enable stakeholders in health care to incorporate miRNA in the clinical policy.
Joint representations of color and form in mouse visual cortex described by random pooling from rods and cones
Authors: Rhim I. , Nauhaus I.
Published: July 2021

Spatial transitions in color can aid any visual perception task, and its neural representation – the “integration of color and form” – is thought to begin at primary visual cortex (V1). An integration of color and form is untested in mouse V1, yet studies show that the ventral retina provides the necessary substrate from green-sensitive rods and UV-sensitive cones. Here, we used two-photon imaging in V1 to measure spatial frequency (SF) tuning along four axes of rod and cone contrast space, including luminance and color. We first reveal that V1’s sensitivity to color is similar to luminance, yet average SF tuning is significantly shifted lowpass for color. Next, guided by linear models, we used SF tuning along all four color axes to estimate the proportion of neurons that fall into classic models of color opponency – “single-”, “double-”, and “non-opponent”. Few neurons (~6%) fit criteria for double-opponency, which are uniquely tuned for chromatic borders. Most of the population can be described as a unimodal distribution ranging from strongly single-opponent to non-opponent. Consistent with recent studies of the rodent and primate retina, our V1 data is well-described by a simple model in which ON and OFF channels to V1 sample the photoreceptor mosaic randomly.
CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion
Authors: Krohannon Alexander , Srivastava Mansi , Rauch Simone , Srivastava Rajneesh , Dickinson Bryan C. , Janga Sarath Chandra
Published: July 2021

Recent discovery of the gene editing system -CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas), has resulted in its widespread use for improved understanding of a variety of biological systems. Cas13, a lesser studied Cas protein, has been repurposed to allow for efficient and precise editing of RNA molecules. The Cas13 system utilizes base complementarity between a crRNA/sgRNA (crispr RNA or single guide RNA) and a target RNA transcript, to preferentially bind to only the target transcript. Unlike targeting the upstream regulatory regions of protein coding genes on the genome, the transcriptome is significantly more redundant, leading to many transcripts having wide stretches of identical nucleotide sequences. Transcripts also exhibit complex three-dimensional structures and interact with an array of RBPs (RNA Binding Proteins), both of which further limit the scope of effective target sequences. As a result, there currently exists no method to predict whether a specific sgRNA will effectively knockdown a transcript. Here we present a novel machine learning and computational tool, CASowary, to predict the efficacy of a sgRNA. We used publicly available RNA knockdown data from Cas13 characterization experiments for 555 sgRNAs targeting the transcriptome in HEK293 cells, in conjunction with transcriptome-wide protein occupancy information on RNA. Our model utilizes a Decision Tree architecture with a set of 112 sequence and target availability features, to classify sgRNA efficacy into one of four classes, based upon expected level of target transcript knockdown. After accounting for noise in the training data set, the noise-normalized accuracy exceeds 70%. Additionally, highly effective sgRNA predictions have been experimentally validated using an independent RNA targeting Cas system -CIRTS, confirming the robustness and reproducibility of our model’s sgRNA predictions. Utilizing transcriptome wide protein occupancy map generated using POP-seq in Hela cells against publicly available protein-RNA interaction map in Hek293 cells, we show that CASowary can predict high quality guides for numerous transcripts in a cell line specific manner. Application of CASowary to whole transcriptomes should enable rapid deployment of CRISPR/Cas13 systems, facilitating the development of therapeutic interventions linked with aberrations in RNA regulatory processes.
Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects Macaques from infection
Authors: Sulbaran Guidenn , Maisonnasse Pauline , Amen Axelle , Guilligay Delphine , Dereuddre-Bosquet Nathalie , Burger Judith A. , Poniman Meliawati , Buisson Marlyse , Dergan Dylon Sebastian , Naninck Thibaut , Lemaître Julien , Gros Wesley , Gallouët Anne-Sophie , Marlin Romain , Bouillier Camille , Contreras Vanessa , Relouzat Francis , Fenel Daphna , Thepaut Michel , Bally Isabelle , Thielens Nicole , Fieschi Franck , Schoehn Guy , van der Werf Sylvie , van Gils Marit J. , Sanders Rogier W. , Poignard Pascal , Le Grand Roger , Weissenhorn Winfried
Published: July 2021

The SARS-CoV-2 pandemic causes an ongoing global health crisis, which requires efficient and safe vaccination programs. Here, we present synthetic SARS-CoV2 S glycoprotein-coated liposomes that resemble in size and surface structure virus-like particles. Soluble S glycoprotein trimers were stabilized by formaldehyde cross-linking and coated onto lipid vesicles (S-VLP). Immunization of cynomolgus macaques with S-VLPs induced high antibody titers and TH1 CD4+ biased T cell responses. Although antibody responses were initially dominated by RBD specificity, the third immunization boosted non-RBD antibody titers. Antibodies showed potent neutralization against the vaccine strain and the Alpha variant after two immunizations and robust neutralization of Beta and Gamma strains. Challenge of animals with SARS-CoV-2 protected all vaccinated animals by sterilizing immunity. Thus, the S-VLP approach is an efficient and safe vaccine candidate based on a proven classical approach for further development and clinical testing.
AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational approximated Landscape
Authors: Sesta Luca , Uguzzoni Guido , Diaz Jorge Fernandez-de-Cossio , Pagnani Andrea
Published: July 2021

We present Annealed Mutational approximated landscape (AMaLa), a new method to infer fitness landscapes from Directed Evolution experiment sequencing data. Directed Evolution experiments typically start from a single wild-type sequence, which undergoes Darwinian in vitro evolution acted via multiple rounds of mutation and selection with respect to a target phenotype. In the last years, Directed Evolution is emerging as a powerful instrument to probe fitness landscapes under controlled experimental condition and, thanks to the use of high-throughput sequencing of the different rounds, as a relevant testing ground to develop accurate statistical models and inference algorithms.

Fitness landscape modeling strategies, either use as input data the enrichment of variants abundances and hence require observing the same variants at different rounds, or they simply assume that the variants at the last sequenced round are the results of a sampling process at equilibrium. AMaLa aims at leveraging effectively the information encoded in the time evolution of all sequenced rounds. To do so, on the one hand we assume statistical sampling independence between sequenced rounds, and on the other we gauge all possible trajectories in sequence space with a time-dependent statistical weight consisting of two contributions: (i) a statistical energy term accounting for the selection process, (ii) a simple generalized Jukes-Cantor model to describe the purely mutational step.

This simple scheme allows us to accurately describe the Directed Evolution dynamics in a concrete experimental setup and to infer a fitness landscape that reproduces correctly the measures of the phenotype under selection (e.g. antibiotic drug resistance), notably outperforming widely used inference strategies. We assess the reliability of AMaLa by showing how the inferred statistical model could be used to predict relevant structural properties of the wild-type sequence, and to reproduce the mutational effects of large scale functional screening not used to train the model.
Uncoupling of the Diurnal Growth Program by Artificial Genome Relaxation in Synechocystis sp. PCC 6803
Authors: Behle Anna , Dietsch Maximilian , Goldschmidt Louis , Murugathas Wandana , Brandt David , Busche Tobias , Kalinowski Jörn , Ebenhöh Oliver , Axmann Ilka M. , Machné Rainer
Published: July 2021

In cyanobacteria DNA supercoiling varies over the diurnal light/dark cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knock-down of gyrase subunits and overexpression of topoisomerase I (TopoI), and characterized the phenotypes. Cell division was blocked, most likely due to inhibition of genomic but not plasmid DNA replication. Cell growth continued to 4-5x of the wildtype cell volume, and metabolic flux was redirected towards glycogen in the TopoI overexpression strain. TopoI induction initially lead to down-regulation of GC-rich and up-regulation of AT-rich genes. The response quickly bifurcated and four diurnal co-expression cohorts (dawn, noon, dusk and night) all responded differently, in part with a circadian (≈ 24 h) pattern. A GC-rich region − 50 bp of transcription start sites is differentially enriched in these four cohorts. We suggest a model where energy- and gyrase-gated transcription of growth genes at the dark/light transition (dawn) generates DNA supercoiling which then facilitates DNA replication and initiates the diurnal transcriptome program.
Characterizing enterotypes in human metagenomics: a viral perspective
Authors: Song Li , Zhang Lu , Fang Xiaodong
Published: July 2021

The diversity and high genomic mutation rates of viral species hinder our understanding of viruses and their contributions to human health. Here we investigated the human fecal virome using previously published sequencing data of 2,690 metagenomes from seven countries. We found that the virome was dominated by double-stranded DNA viruses, and young children and adults showed dramatic differences in their fecal enterovirus composition. Beta diversity showed there were significantly higher distances to centroids in individuals with severe phenotypes, such as cirrhosis. In contrast, there were no significant differences in lengths to centroids or viral components between patients with mild phenotypes, such as hypertension. Enterotypes showed the same specific viruses and enrichment direction after independent determination of enterotypes in various projects. Confounding factors, such as different sequencing platforms and library construction, did not result in a batch effect to confuse enterotype assignment. The gut virome composition pattern could be described by two viral enterotypes, which supported a discrete, rather than a gradient, distribution. Compared with enterotype 2, enterotype 1 had a higher viral count and Shannon index, but a lower beta diversity, indicating more resistance to the external environment’s harmful effects. Disease was usually accompanied by a viral enterotype disorder. However, a sample outside of the enterotyping mathematical space of enterotype database did not necessarily indicate sickness. Therefore, the background context must be carefully considered when using a viral enterotype as a biomarker for disease prediction. The disease, second only to the enterotype, explains significant variation in viral community composition, implying that double-stranded DNA is relevant to human health. Our results of investigating a baseline viral database highlight important insights into the virome composition of human ecosystems, and provide an alternate biomarker for early disease screening.
Effect of stimulation time on the expression of human macrophage polarization markers
Authors: Purcu Duygu Unuvar , Korkmaz Asli , Gunalp Sinem , Helvaci Derya Goksu , Erdal Yonca , Dogan Yavuz , Suner Asli , Wingender Gerhard , Sag Duygu
Published: July 2021

Macrophages are highly plastic cells that can polarize into functionally distinct subsetsin vivoandin vitroin response to environmental signals. The development of protocols to model macrophage polarizationin vitrogreatly contributes to our understanding of macrophage biology. Macrophages are divided into two main groups: Pro-inflammatory M1 macrophages (classically activated) and anti-inflammatory M2 macrophages (alternatively activated), based on several key surface markers and the production of inflammatory mediators. However, the expression of these common macrophage polarization markers is greatly affected by the stimulation time used. Unfortunately, there is no consensus yet regarding the optimal stimulation times for particular macrophage polarization markers inin vitroexperiments. This situation is problematic, (i) as analysing a particular marker at a suboptimal time point can lead to false-negative results, and (ii) as it clearly impedes the comparison of different studies. Using human monocyte-derived macrophages (MDMs)in vitro, we analysed how the expression of the main polarization markers for M1 (CD64, CD86, CXCL9, CXCL10, HLA-DR, IDO1, IL1β, IL12, TNF), M2a (CD200R, CD206, CCL17, CCL22, IL-10, TGM2), and M2c (CD163, IL-10, TGFβ) macrophages changes over time at mRNA and protein levels. Our data establish the most appropriate stimulation time for the analysis of the expression of human macrophage polarization markersin vitro. Providing such a reference guide will likely facilitate the investigation of macrophage polarization and its reproducibility.
Temporal Dynamics of HCMV Gene Expression in Lytic and Latent Infections
Authors: Rozman Batsheva , Nachshon Aharon , Samia Roi Levi , Lavi Michael , Schwartz Michal , Stern-Ginossar Noam
Published: July 2021

Primary infection with Human cytomegalovirus (HCMV) results in a persistent lifelong infection due to its ability to establish latent infection. During productive HCMV infection, viral genes are expressed in a coordinated cascade that is characteristic of all herpesviruses and traditionally relies on the dependencies of viral genes on protein synthesis and viral DNA replication. In contrast, the transcriptional landscape associated with HCMV latency is still disputed and poorly understood. Here, we examine viral transcriptomic dynamics during the establishment of both productive and latent HCMV infections. Our temporal measurements reveal that viral gene expression dynamics along productive infection and their dependencies on protein synthesis and viral DNA replication, do not fully align. This illustrates that the regulation of herpesvirus genes does not represent a simple sequential transcriptional cascade, and surprisingly, many viral genes are regulated by multiple independent modules. Using our improved classification of viral gene expression kinetics in conjunction with transcriptome-wide measurements of the effects of a wide array of chromatin modifiers, we unbiasedly show that a defining characteristic of latent cells is the unique repression of immediate early (IE) genes. Altogether, our findings provide an elaborate definition of HCMV gene expression patterns and reveal novel principles that govern viral gene expression in lytic and latent infection states.
NMR spectroscopy of a single mammalian embryo
Authors: Sivelli Giulia , Conley Gaurasundar M. , Herrera Carolina , Marable Kathryn , Rodriguez Kyle J. , Bollwein Heinrich , Sudano Mateus J. , Brugger Jürgen , Simpson Andre J. , Boero Giovanni , Grisi Marco
Published: July 2021

The resolving power, chemical sensitivity and non-invasive nature of NMR has made it an established technique for in vivo studies of large organisms both for research and clinical applications. These features would clearly be beneficial at the nanoliter scale (nL), typical of early development of mammalian embryos, microtissues and organoids, the scale where the building blocks of complex organisms could be observed. However, the handling of such small samples (about 100 micrometers) and sensitivity issues have prevented the widespread adoption of NMR. Recently we have shown how these limitations can be overcome with ultra-compact single-chip probes. In this article we show that such probes have sufficient sensitivity to detect and resolve NMR signals from individual bovine pre-implantation embryos. In less than 1 hour these spherical samples of just 130-190 micrometers produce distinct spectral peaks, largely originating from lipids contained inside them. We further observe how the spectral features, namely the peak intensities, vary from one sample to another despite their optical and morphological similarities.
SIRV: Spatial inference of RNA velocity at the single-cell resolution
Authors: Abdelaal Tamim , Grossouw Laurens M. , Pasterkamp R. Jeroen , Lelieveldt Boudewijn P.F. , Reinders Marcel J.T. , Mahfouz Ahmed
Published: July 2021

RNA Velocity allows the inference of cellular differentiation trajectories from single-cell RNA sequencing (scRNA-seq) data. It would be highly interesting to study these differentiation dynamics in the spatial context of tissues. Estimating spatial RNA velocities is, however, limited by the inability to spatially capture spliced and unspliced mRNA molecules in high-resolution spatial transcriptomics. We present SIRV, a method to spatially infer RNA velocities at the single-cell resolution by enriching spatial transcriptomics data with the expression of spliced and unspliced mRNA from reference scRNA-seq data. We used SIRV to infer spatial differentiation trajectories in the developing mouse brain, including the differentiation of midbrain-hindbrain boundary cells and marking the forebrain origin of the cortical hem and diencephalon cells. Our results show that SIRV reveals spatial differentiation patterns not identifiable with scRNA-seq data alone. Additionally, we applied SIRV to mouse organogenesis data and obtained robust spatial differentiation trajectories. Finally, we verified the spatial RNA velocities obtained by SIRV using 10x Visium data of the developing chicken heart and MERFISH data from human osteosarcoma cells. Altogether, SIRV allows the inference of spatial RNA velocities at the single-cell resolution to facilitate studying tissue development.
Model predicts the impact of root system architecture on soil water infiltration
Authors: Mair Andrew , Dupuy Lionel X , Ptashnyk Mariya
Published: July 2021

There is strong experimental evidence that root systems substantially change the saturated hydraulic conductivity of soil. However, the mechanisms by which roots affect soil hydraulic properties remain largely unknown. In this work, we made the hypothesis that preferential soil moisture transport occurs along the axes of roots, and that this is what changes a soil’s saturated hydraulic conductivity. We modified Richards’ equation to incorporate the preferential flow of soil moisture along the axes of roots. Using the finite element method and Bayesian optimisation, we developed a pipeline to calibrate our model with respect to a given root system. When applied to simulated root systems, the pipeline successfully predicted the pore-water pressure profiles corresponding to saturated hydraulic conductivity values, observed by Leung et al. (2018), for soils vegetated with willow and grass. Prediction accuracy improved for root systems with more realistic architectures, therefore suggesting that changes in saturated hydraulic conductivity are a result of roots enabling preferential soil moisture transport along their axes. The model proposed in this work improves our ability to predict moisture transport through vegetated soil and could help optimise irrigation, forecast flood events and plan landslide prevention strategies.
Regulatory start-stop elements in 5’ untranslated regions pervasively modulate translation
Authors: Rendleman Justin , Haizel Solomon , Wu Shaohuan , Liu Junjie , Ge Xinyi , Zou Huijing , Mohammad Mahabub Pasha , Pressler Matthew , Maity Shuvadeep , Hronová Vladislava , Gao Zhaofeng , Herrmannová Anna , Lei Amy , Allgoewer Kristina , Sultanov Daniel , Hinckley Will Edward , Cheng Ziyue , Shelby Lauren , Szkop Krzysztof J. , Topisirovic Ivan , Larsson Ola , Hatzoglou Maria , Valášek Leoš Shivaya , Vogel Christine
Published: July 2021

Sequence elements within the 5’ untranslated region (UTR) of eukaryotic genes, e.g. upstream open reading frames (uORFs), control translation of eukaryotic genes. We describe an element consisting of a start codon immediately followed by a stop codon which is distinct from uORFs in the lack of an elongation step. Start-stops have been described for specific cases, but their widespread impact has been overlooked. Start-stop elements occur in the 5’UTR of 1, 417 human genes and are more often occupied with a ribosome than canonical uORFs or control sequences. Start-stops efficiently halt ribosomes without evidence for accelerated RNA turnover, therefore acting as a barrier for the scanning of the small ribosomal subunit and repressing downstream translation. Our results suggest a model by which the ribosome undergoes repeated cycles of termination and partial ribosomal recycling, during which the large subunit detaches, but the 40S subunit with the Met-tRNAiMetremains associated with the mRNA to be rejoined by the 60S subunit. Start-stop elements occur in many transcription factors and signaling genes, and affect cellular fate via different routes. We investigate the start-stop element in several genes, i.e.MORF4L1,SLC39A1, andPSPC1, and in more detail inATF4.
Emergence of a novel mobile RND-type efflux pump gene cluster,tmexC3D2-toprJ1b, inPseudomonasspecies
Authors: Maehana Shotaro , Eda Ryotaro , Niida Nagi , Hirabayashi Aki , Sakai Kouji , Furukawa Takashi , Sei Kazunari , Kitasato Hidero , Suzuki Masato
Published: July 2021

Tigecycline exhibits promising activity against multidrug-resistant Gram-negative bacteria (MDR-GNB), whose infections are difficult to treat with antimicrobials. However, mobile tigecycline resistance genes, such astmexCD-toprJ, have emerged in Enterobacterales isolated in China, Vietnam, and possibly other countries in the world. In this study, we investigated tigecycline-nonsusceptible GNB in Japan. Eight tigecycline- and carbapenem-nonsusceptible isolates ofPseudomonas alcaligeneswere obtained from sewage water from a medical institution in Japan in 2020. Whole genome analysis of allP. alcaligenesisolates was performed using short-read sequencing, and the isolate KAM426 was further analyzed using long-read sequencing. For important antimicrobial resistance genes, analysis of surrounding structures and comparison with similar sequences in the public genome database were performed. We identified a novel hybrid type oftmexCD-toprJgene cluster,tmexC3D2-toprJ1bconsisting oftmexC3,tmexC2, andtoprJ1b, in phylogenetically clonal isolates ofP. alcaligenes. The complete genome sequence of KAM426 revealed that this isolate co-harborstmexC3D2-toprJ1band two copies of the carbapenemase geneblaIMP-1on the chromosome.tmexC3D2-toprJ1bin KAM426 was flanked by the IS5/IS1182family transposase gene, suggesting that the gene cluster was acquired by horizontal gene transfer (HGT).tmexC3D2-toprJ1bseemed to have spread to otherPseudomonasspecies such asPseudomonas aeruginosavia HGT mediated by mobile gene elements such as a plasmid. This study identifiedtmexCD-toprJ-like tigecycline resistance genes in Japan for the first time and suggests that diversetmexCD-toprJ-like gene clusters, includingtmexC3D2-toprJ1b, have spread among MDR-GNB worldwide. Further epidemiological genomic studies in clinical and environmental settings are needed.
Trehalose increases tomato drought tolerance, induces defenses, and increases resistance to bacterial wilt disease
Authors: MacIntyre April M. , Meline Valerian , Gorman Zachary , Augustine Steven P. , Dye Carolyn J. , Hamilton Corri D. , Iyer-Pascuzzi Anjali S. , Kolomiets Michael V. , McCulloh Katherine A. , Allen Caitilyn
Published: July 2021

Ralstonia solanacearumcauses bacterial wilt disease, leading to severe crop losses. Xylem sap fromR. solanacearum-infected tomato is enriched in the disaccharide trehalose. Water-stressed plants also accumulate trehalose, which increases drought tolerance via abscisic acid (ABA) signaling. BecauseR. solanacearum-infected plants suffer reduced water flow, we hypothesized that bacterial wilt physiologically mimics drought stress, which trehalose could mitigate. We found thatR. solanacearum-infected plants differentially expressed drought-associated genes, including those involved in ABA and trehalose metabolism, and had more ABA in xylem sap. Consistent with this, treating tomato roots with ABA reduced both stomatal conductance and stem colonization byR. solanacearum. Treating roots with trehalose increased xylem sap ABA and reduced plant water use by lowering stomatal conductance and temporarily improving water use efficiency. Trehalose treatment also upregulated expression of salicylic acid (SA)-dependent tomato defense genes; increased xylem sap levels of SA and other antimicrobial compounds; and increased bacterial wilt resistance of SA-insensitiveNahGtomato plants. Additionally, trehalose treatment increased xylem concentrations of jasmonic acid and related oxylipins. Finally, trehalose-treated plants were substantially more resistant to bacterial wilt disease. Together, these data show that exogenous trehalose reduced both water stress and bacterial wilt disease and triggered systemic disease resistance, possibly through a Damage Associated Molecular Pattern (DAMP) response pathway. This suite of responses revealed unexpected linkages between plant responses to biotic and abiotic stress and suggested thatR. solanacearum-infected plants increase trehalose to improve water use efficiency and increase wilt disease resistance. The pathogen may degrade trehalose to counter these efforts. Together, these results suggest that treating tomatoes with exogenous trehalose could be a practical strategy for bacterial wilt management.
Caldendrin represses neurite regeneration via a sex-dependent mechanism in sensory neurons
Authors: Lopez Josue A. , Yamamoto Annamarie , Vecchi Joseph T. , Hagen Jussara , Lee Amy
Published: July 2021

Caldendrin is a calmodulin-like Ca2+binding protein that is expressed primarily in neurons and regulates multiple effectors including Cav1 L-type Ca2+channels. Here, we tested the hypothesis that caldendrin regulates Cav1-dependent pathways that repress neurite growth in dorsal root ganglion neurons (DRGNs). By immunofluorescence, caldendrin was localized in medium- and large-diameter DRGNs. Consistent with an inhibitory effect of caldendrin on neurite growth, neurite initiation and growth was enhanced in dissociated DRGNs from caldendrin knockout (KO) mice compared to those from wild type (WT) mice. In anin vitroaxotomy assay, caldendrin KO DRGNs grew longer neurites via a mechanism that was more sensitive to inhibitors of transcription as compared to WT DRGNs. Strong depolarization, which normally represses neurite growth through activation of Cav1 channels, had no effect on neurite growth in DRGN cultures from female caldendrin KO mice. Remarkably, DRGNs from caldendrin KO males were no different from those of WT males in terms of depolarization-dependent neurite growth repression. We conclude that caldendrin opposes neurite regeneration and growth, and this involves coupling of Cav1 channels to growth-inhibitory pathways in DRGNs of females but not males. Our findings suggest that caldendrin KO mice represent an ideal model in which to interrogate the transcriptional pathways controlling neurite regeneration and how these pathways may differ in males and females.
Newly identified parasitic nematode beta-tubulin alleles confer resistance to benzimidazoles
Authors: Dilks Clayton M. , Koury Emily J. , Buchanan Claire M. , Andersen Erik C.
Published: July 2021

Infections by parasitic nematodes cause large health and economic burdens worldwide. We use anthelmintic drugs to reduce these infections. However, resistance to anthelmintic drugs is extremely common and increasing worldwide. It is essential to understand the mechanisms of resistance to slow its spread. Recently, four new parasitic nematode beta-tubulin alleles have been identified in benzimidazole (BZ) resistant parasite populations: E198I, E198K, E198T, and E198stop. These alleles have not been tested for the ability to confer resistance or for any effects that they might have on organismal fitness. We introduced these four new alleles into the sensitive C. elegans laboratory-adapted N2 strain and exposed these genome-edited strains to both albendazole and fenbendazole. We found that all four alleles conferred resistance to both BZ drugs. Additionally, we tested for fitness consequences in both control and albendazole conditions over seven generations in competitive fitness assays. We found that none of the edited alleles had deleterious effects on fitness in control conditions and that all four alleles conferred strong and equivalent fitness benefits in BZ drug conditions. Because it is unknown if previously validated alleles confer a dominant or recessive BZ resistance phenotype, we tested the phenotypes caused by five of these alleles and found that none of them conferred a dominant BZ resistance phenotype. Accurate measurements of resistance, fitness effects, and dominance caused by the resistance alleles allow for the generation of better models of population dynamics and facilitate control practices that maximize the efficacy of this critical anthelmintic drug class.

Highlights

Four newly identified parasitic nematode beta-tubulin alleles confer benzimidazole resistance

The four newly identified alleles do not confer deleterious fitness consequences

Five beta-tubulin alleles confer recessive benzimidazole resistance

Graphical abstract
Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus
Authors: Kreiner J.M. , Caballero Amalia , Wright S.I. , Stinchcombe J.R.
Published: July 2021

The relative role of hybridization, de novo evolution, and standing variation in weed adaptation to agricultural environments is largely unknown. In Amaranthus tuberculatus, a widespread North American agricultural weed, adaptation is likely influenced by recent secondary contact and admixture of two previously isolated subspecies. We characterized the extent of adaptation and phenotypic differentiation accompanying the spread of A. tuberculatus into agricultural environments and the contribution of subspecies divergence. We generated phenotypic and whole-genome sequence data from a manipulative common garden experiment, using paired samples from natural and agricultural populations. We found strong latitudinal, longitudinal, and sex differentiation in phenotypes, and subtle differences among agricultural and natural environments that were further resolved with ancestry inference. The transition into agricultural environments has favoured southwestern var. rudis ancestry that leads to higher biomass and environment-specific phenotypes: increased biomass and earlier flowering under reduced water availability, and reduced plasticity in fitness-related traits. We also detected de novo adaptation to agricultural habitats independent of ancestry effects, including marginally higher biomass and later flowering in agricultural populations, and a time to germination home advantage. Therefore, the invasion of A. tuberculatus into agricultural environments has drawn on adaptive variation across multiple timescales—through both preadaptation via the preferential sorting of var. rudis ancestry and de novo local adaptation.