bluuebunny/crossref_metadata_2025 huggingface dataset:
Illuminating the lineage-specific diversification of resin glycoside acylsugars in the morning glory (Convolvulaceae) family using computational metabolomics
Authors: Kruse Lars H , Bennett Alexandra A , Mahood Elizabeth H , Lazarus Elena , Park Se Jin , Schroeder Frank , Moghe Gaurav D
Published: January 2022

Acylsugars are a class of plant defense compounds produced across many distantly related families. Members of the horticulturally important morning glory (Convolvulaceae) family produce a diverse subclass of acylsugars called resin glycosides (RGs), which comprise oligosaccharide cores, hydroxyacyl chain(s), and decorating aliphatic and aromatic acyl chains. While many RG structures are characterized, the extent of structural diversity of this class in different genera and species is not known. In this study, we asked whether there has been lineage-specific diversification of RG structures in different Convolvulaceae species that may suggest diversification of the underlying biosynthetic pathways. Liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) was performed from root and leaf extracts of 26 species sampled in a phylogeny-guided manner. LC–MS/MS revealed thousands of peaks with signature RG fragmentation patterns with one species producing over 300 signals, mirroring the diversity in Solanaceae-type acylsugars. A novel RG from Dichondra argentea was characterized using nuclear magnetic resonance spectroscopy, supporting previous observations of RGs with open hydroxyacyl chains instead of closed macrolactone ring structures. Substantial lineage-specific differentiation in utilization of sugars, hydroxyacyl chains, and decorating acyl chains was discovered, especially among Ipomoea and Convolvulus—the two largest genera in Convolvulaceae. Adopting a computational, knowledge-based strategy, we further developed a high-recall workflow that successfully explained ~72% of the MS/MS fragments, predicted the structural components of 11/13 previously characterized RGs, and partially annotated ~45% of the RGs. Overall, this study improves our understanding of phytochemical diversity and lays a foundation for characterizing the evolutionary mechanisms underlying RG diversification.
The reference genome of Camellia chekiangoleosa provides insights into Camellia evolution and tea oil biosynthesis
Authors: Shen Teng-fei , Huang Bin , Xu Meng , Zhou Peng-yan , Ni Zhou-xian , Gong Chun , Wen Qiang , Cao Fu-liang , Xu Li-An
Published: January 2022

Camellia oil extracted from Camellia seeds is rich in unsaturated fatty acids and secondary metabolites beneficial to human health. However, no oil-tea tree genome has yet been published, which is a major obstacle to investigating the heredity improvement of oil-tea trees. Here, using both Illumina and PicBio sequencing technologies, we present the first chromosome-level genome sequence of the oil-tea tree species Camellia chekiangoleosa Hu. (CCH). The assembled genome consists of 15 pseudochromosomes with a genome size of 2.73 Gb and a scaffold N50 of 185.30 Mb. At least 2.16 Gb of the genome assembly consists of repetitive sequences, and the rest involves a high-confidence set of 64 608 protein-coding gene models. Comparative genomic analysis revealed that the CCH genome underwent a whole-genome duplication event shared across the Camellia genus at ~57.48 MYA and a γ-WGT event shared across all core eudicot plants at ~120 MYA. Gene family clustering revealed that the genes involved in terpenoid biosynthesis have undergone rapid expansion. Furthermore, we determined the expression patterns of oleic acid accumulation- and terpenoid biosynthesis-associated genes in six tissues. We found that these genes tend to be highly expressed in leaves, pericarp tissues, roots, and seeds. The first chromosome-level genome of oil-tea trees will provide valuable resources for determining Camellia evolution and utilizing the germplasm of this taxon.
Outcomes of Ileoanal Pouch Anastomosis in Pediatric Ulcerative Colitis Are Worse in the Modern Era: A Time Trend Analysis Outcomes Following Ileal Pouch–Anal Anastomosis in Pediatric Ulcerative Colitis
Authors: Runde Joseph , Erondu Amarachi , Akiyama Shintaro , Traboulsi Cindy , Rai Victoria , Glick Laura R , Yi Yangtian , Ollech Jacob E , Cohen Russell D , Skowron Kinga B , Hurst Roger D , Umanskiy Konstatin , Shogan Benjamin D , Hyman Neil H , Rubin Michele A , Dalal Sushila R , Sakuraba Atsushi , Pekow Joel , Chang Eugene B , Rubin David T
Published: January 2022

Background

Despite significant differences in surgical outcomes between pediatric and adult patients with ulcerative colitis (UC) undergoing colectomy, counseling on pediatric outcomes has largely been guided by data from adults. We compared differences in pouch survival between pediatric and adult patients who underwent total proctocolectomy with ileal pouch–anal anastomosis (IPAA).

Methods

This was a retrospective single-center study of patients with UC treated with IPAA who subsequently underwent pouchoscopy between 1980 and 2019. Data were collected via electronic medical records. We stratified the study population based on age at IPAA. Differences between groups were assessed using t tests and chi-square tests. Kaplan-Meier curves were used to compare survival probabilities. Differences between groups were assessed using a log-rank test.

Results

We identified 53 patients with UC who underwent IPAA before 19 years of age and 329 patients with UC who underwent IPAA at or after 19 years of age. Subjects who underwent IPAA as children were more likely to require anti-tumor nerosis factor (TNF) postcolectomy compared with adults (41.5% vs 25.8%; P < .05). Kaplan-Meier estimates revealed that pediatric patients who underwent IPAA in the last 10 years had a 5-year pouch survival probability that was 28% lower than that of those who underwent surgery in the 1990s or 2000s (72% vs 100%; P < .001). Further, children who underwent IPAA and received anti-TNF therapies precolectomy had the most rapid progression to pouch failure when compared with anti-TNF–naive children and with adults who were either exposed or naive precolectomy (P < .05).

Conclusions

There are lower rates of pouch survival for children with UC who underwent IPAA following the uptake of anti-TNF therapy compared with both historical pediatric control subjects and contemporary adults.
Biphasic mineralized collagen-based composite scaffold for cranial bone regeneration in developing sheep
Authors: Zheng Jingchuan , Zhao Zhijun , Yang Yongdong , Wang Shuo , Zhao Yonggang , Xiong Yang , Yang Shuhui , Qiu Zhiye , Song Tianxi , Zhang Chunyang , Wang Xiumei
Published: January 2022

Appropriate mechanical support and excellent osteogenic capability are two essential prerequisites of customized implants for regenerating large-sized cranial bone defect. Although porous bone scaffolds have been widely proven to promote bone regeneration, their weak mechanical properties limit the clinical applications in cranioplasty. Herein, we applied two previously developed mineralized collagen-based bone scaffolds (MC), porous MC (pMC) and compact MC (cMC) to construct a biphasic MC composite bone scaffold (bMC) to repair the large-sized cranial bone defect in developing sheep. A supporting frame composed of cMC phase in the shape of tic–tac–toe structure was fabricated first and then embedded in pMC phase. The two phases had good interfacial bond, attributing to the formation of an interfacial zone. The in vivo performance of the bMC scaffold was evaluated by using a cranial bone defect model in 1-month-old sheep. The computed tomography imaging, X-ray scanning and histological evaluation showed that the pMC phase in the bMC scaffold, similar to the pMC scaffold, was gradually replaced by the regenerative bone tissues with comprehensively increased bone mineral density and complete connection of bone bridge in the whole region. The cMC frame promoted new bone formation beneath the frame without obvious degradation, thus providing appropriate mechanical protection and ensuring the structural integrity of the implant. In general, the sheep with bMC implantation exhibited the best status of survival, growth and the repair effect. The biphasic structural design may be a prospective strategy for developing new generation of cranioplasty materials to regenerate cranial bone defect in clinic.
Non-Ischemic, Non-Hypoxic Myocardial Injury, and Long-Term Mortality in Patients with Coronavirus Disease 2019: A Retrospective Cohort Study
Authors: Li Fajiu , Zhu Xijie , Zhu Ziyang , Yang Yinjian , Tian Zhuang , Wang Duolao , Chen Shi , Gao Xiaoyan , Xu Yalin , Zhang Bo , Yu Wei , Liu Min , Xu Xiqi , Li Chenghong , Zhang Shuyang
Published: January 2022

Objective:

Cardiac damage is commonly reported in patients with coronavirus disease 2019 (COVID-19) but its prevalence and impact on the long-term survival of patients remain uncertain. This study aimed to explore the prevalence of myocardial injury and assess its prognostic value in patients with COVID-19.

Methods:

A single-center, retrospective cohort study was performed at the Affiliated Hospital of Jianghan University. Data from 766 patients with confirmed COVID-19 who were hospitalized from December 27, 2019 to April 25, 2020 were collected. Demographic, clinical, laboratory, electrocardiogram, treatment data and all-cause mortality during follow-up were collected and analyzed.

Results:

Of the 766 patients with moderate to critically ill COVID-19, 86 (11.2%) died after a mean follow-up of 72.8 days. Myocardial injury occurred in 94 (12.3%) patients. The mortality rate was 64.9% (61/94) and 3.7% (25/672) in patients with and without myocardial injury, respectively. Cox regression showed that myocardial injury was an independent risk factor for mortality (hazard ratio: 8.76, 95% confidence interval: 4.76–16.11, P 
< 0.001). Of the 90 patients with myocardial injury with electrocardiogram results, sinus tachycardia was present in 29, bundle branch block in 26, low voltage in 10, and abnormal T-wave in 53.

Conclusions:

COVID-19 not only involves pneumonia but also cardiac damage. Myocardial injury is a common complication and an independent risk factor for mortality in COVID-19 patients.
Utilizing a Comprehensive Wound Care Team to Lower Hospital-Acquired Pressure Injuries in an Academic Public Hospital
Authors: Powell Lauren E. , Winn Elisa , Andersen Emily S. , Pozez Andrea L.
Published: January 2022

PURPOSE:

Hospital-acquired pressure injuries (HAPIs) have significant impacts on patient morbidity and mortality, with approximately 2.5 million patients treated for pressure-related injuries annually.1 This study aimed to describe the influence of a comprehensive wound care team on HAPIs over an 8-year period.

DESIGN:

Retrospective cohort study.

SUBJECTS AND SETTING:

All inpatients at an academic public hospital system with HAPIs during the study period from May 2012 to February 2020.

METHODS:

Data on wound stage, location, infection, medical device location if applicable, and risk factors were recorded from medical records. A 1-way analysis of variance was performed to assess for significance of mean number of cases, National Pressure Injury Advisory Panel (NPIAP) stage on initial presentation, and mean number of medical device-related wounds by year.

RESULTS:

A total of 957 cases were included. The median stage of pressure injury on assessment was 2, with the mean NPIAP stage declining from 2012 to 2020 (P = .003). Thirty-three percent of pressure injuries were attributed to medical devices, most commonly endotracheal tubing. The most common site of pressure injury was the sacrum (33.6%).

CONCLUSION:

Creation of a comprehensive wound care team within our academic public hospital system demonstrated a significant decline in device-related and pressure injury cases over the past 8 years. The wound care team focused on frequent assessment, education, and evidence-based treatment to lower these HAPI events.
Surveillance of SARS-CoV-2 RNA in open-water sewage canals contaminated with untreated wastewater in resource-constrained regions
Authors: Basu Paramita , Choudhury Sandeepan , Shridhar Varsha , Huilgol Poorva , Roychoudhury Samrat , Nandi Indranil , Chaudhuri Angela , Mitra Arindam
Published: January 2022

Sewage-based surveillance for COVID-19 has been described in multiple countries and multiple settings. However, nearly all are based on testing sewage treatment plant inflows and outflows using structured sewage networks and treatment systems. Many resource-limited countries worldwide have open canals, lakes and other such waste-contaminated water bodies that act as a means of sewage effluent discharge. These could serve as hyperlocal testing points for detecting COVID-19 incidence using the effluents from nearby communities. However, a sensitive, robust and economical method of SARS-CoV-2 RNA detection from open waste contaminated water bodies in resource-constrained regions is currently lacking. A protocol employed in Bangalore, India, where SARS-CoV-2 RNA levels were evaluated using two open canal systems during the first and second waves in the present study. SARS-CoV-2 RNA was measured using two strategies: a modified TrueNATTM microchip-based rapid method and traditional real-time reverse transcription-PCR (rRT-PCR), which were compared for analytical sensitivity, cost and relative ease of use. SARS-CoV-2 RNA levels were detected at lower levels during the earlier half compared to the later half of the first wave in 2020. The opposite trend was seen in the second wave in 2021. Interestingly, the change in RNA levels corresponded with the community burden of COVID-19 at both sites. The modified TrueNATTM method yielded concordant results to traditional rRT-PCR in sensitivity and specificity and cost. It provides a simple, cost-effective method for detecting and estimating SARS-CoV-2 viral RNA from open-water sewage canals contaminated with human excreta and industrial waste that can be adopted in regions or countries that lack structured sewage systems.
Genetic variations in the long control region of human papillomavirus type 16 isolates from India: implications for cervical carcinogenesis
Authors: Mane Arati , Limaye Sanket , Patil Linata , Kulkarni-Kale Urmila
Published: January 2022

Introduction. Infection with high-risk human papillomavirus (HPV) types, specifically HPV type 16 (HPV16), is considered to be the most important risk factor in the development of cervical intraepithelial neoplasia and cancer. The long control region (LCR) is a noncoding region that comprises approximately 10 % of the HPV genome and contains regulatory elements for viral transcription and replication. Sequence variations in LCR may impact on the replication efficiency and oncogenic potential of the virus.

Gap statement. Studies documenting variations in LCR of HPV16 isolates pertaining to cervical neoplastic status in India are limited.

Aim. The present study was designed to characterize variations in the LCR of Indian isolates of HPV16 and study their association with cervical disease grades.

Methodology. The LCR was amplified and sequenced from HPV16 positive cervical samples belonging to different cervical disease grades. Sequences were aligned to identify variations and potential transcription factor binding sites (TFbs) were predicted using the JASPAR database in addition to phylogenetic studies.

Results. Among the 163 HPV16 isolates analysed, 47 different nucleotide variations were detected in the LCR, of which 25 are reported for first time in Indian isolates. Point mutations were detected in 35/54 (64.8 %) samples with normal cervical status, 44/50 (88 %) samples with low-grade cervical disease and 53/59 (89.8 %) samples with high-grade cervical disease. Variations T6586C, G6657A and T6850G were significantly associated with high-grade cervical status. Thirteen LCR variations were detected in the binding sites for CEBPB, ETS1, JUN, MYB, NFIL3, PHOX2A and SOX9 transcription factors.

Conclusion. The present study helped to identify unique variations in the LCRs of HPV16 Indian isolates. The variations in the A4 sub-lineage were significantly associated with high-grade disease status. The isolates belonging to the A4 and D3 sub-lineages harboured mutations in putative TFbs, implying a potential impact on viral replication and progression to cervical cancer.
Comparison of sequential therapy with concomitant therapy in first-line treatment of Helicobacter pylori: an updated meta-analysis
Authors: Wang Keliang , Lou Dandi , Dai Wei , Fu Rongrong , Ma Zhenhua
Published: January 2022

Sequential therapy (ST) and concomitant therapy (CT) are common first-line treatments for

Helicobacter pylori

(HP). This study aimed to assess the efficiency and safety of ST and CT in the first-line treatment of HP by comparing their clinical outcomes. Two authors independently searched PubMed, EBSCO, Web of Science and the Cochrane Library for all the relevant articles published before March 2021 to compare the clinical outcomes of HP patients undergoing ST or CT. The primary outcome measures were HP eradication rates and adverse events (AEs). This meta-analysis included 24 articles with 7531 HP patients. CT was better than ST in eradicating HP from per-protocol analysis (PP) (RR=0.96, P<0.001) and modified intent-to-treat analysis (MITT) (RR=0.94, P=0.005). Compared with non-Asia, CT demonstrated more apparent advantages than ST in Asia. CT treated with lansoprazole, pantoprazole and esomeprazole outperformed ST treated with the same PPIs. CT for 10 days and ST for 14 days were the better choices of course of treatment. The incidence rates of AEs were significantly higher in CT than in ST for diarrhoea (RR=0.65, P<0.001), vomiting (RR=0.68, P=0.03), dysgeusia (RR=0.83, P=0.03) and dizziness (RR=0.77, P=0.05). Both ST and CT are safe and effective first-line treatments for HP. Although the AEs were more frequent with CT than ST, CT was superior to ST, especially in Asia. The effect of various PPIs varied in various therapies. The best course of treatment was 10 days for CT and 14 days for ST.
Trehalose biosynthetic gene otsB of Corynebacterium glutamicum is regulated by whcE in response to oxidative stress
Authors: Park Jung Chul , Jeong Haeri , Kim Younhee , Lee Heung-Shick
Published: January 2022

The gene whcE of

Corynebacterium glutamicum

plays a positive role in oxidative stress responses and the WhcE protein interacts with SpiE. By utilizing 2D-PAGE analysis, we identified the otsB gene to be under the control of whcE. The transcription of otsB, encoding trehalose 6-phosphatase, was stimulated by oxidative stress, and whcE and spiE were involved in diamide-mediated transcriptional stimulation. The ΔotsB strain was created and found to be sensitive to the thiol-specific oxidant diamide, suggesting a role of the gene in stress responses. Genes located upstream of otsB, such as NCgl2534 and otsA, formed an operon and purified WhcE was able to bind to the promoter region of the operon (PNCgl2534), but the binding was only possible in the presence of the oxidant diamide. In addition, the transcriptional activation of PNCgl2534 by WhcE was demonstrated in in vivo assays and the transcription was stimulated in cells exposed to the oxidant diamide. These findings indicate that WhcE is a transcriptional activator, and otsB, which is involved in trehalose biosynthesis, has a role in oxidative stress responses in

C. glutamicum

.
Validation of a clinical and genetic model for predicting severe COVID-19
Authors: Dite Gillian S. , Murphy Nicholas M. , Spaeth Erika , Allman Richard ,   Lifelines Corona Research Initiative
Published: January 2022

Using nested case–control data from the Lifelines COVID-19 cohort, we undertook a validation study of a clinical and genetic model to predict the risk of severe COVID-19 in people with confirmed COVID-19 and in people with confirmed or self-reported COVID-19. The model performed well in terms of discrimination of cases and controls for all ages (area under the receiver operating characteristic curve [AUC] = 0.680 for confirmed COVID-19 and AUC = 0.689 for confirmed and self-reported COVID-19) and in the age group in which the model was developed (50 years and older; AUC = 0.658 for confirmed COVID-19 and AUC= 0.651 for confirmed and self-reported COVID-19). There was no evidence of over- or under-dispersion of risk scores but there was evidence of overall over-estimation of risk in all analyses (all P < 0.0001). In the light of large numbers of people worldwide remaining unvaccinated and continuing uncertainty regarding vaccine efficacy over time and against variants of concern, identification of people at high risk of severe COVID-19 may encourage the uptake of vaccinations (including boosters) and the use of non-pharmaceutical inventions.
Ulcerative Colitis Host-Microbiome Response to Hyperbaric Oxygen Therapy
Authors: Gonzalez Carlos G. , Mills Robert H. , Kordahi Melissa C. , Carrillo-Terrazas Marvic , Secaira-Morocho Henrry , Widjaja Christella E. , Tsai Matthew S. , Mittal Yash , Yee Brian A. , Vargas Fernando , Weldon Kelly , Gauglitz Julia M. , Delaroque Clara , Sauceda Consuelo , Rossitto Leigh-Ana , Ackermann Gail , Humphrey Gregory , Swafford Austin D. , Siegel Corey A. , Buckey Jay C. , Raffals Laura E. , Sadler Charlotte , Lindholm Peter , Fisch Kathleen M. , Valaseck Mark , Suriawinata Arief , Yeo Gene W. , Ghosh Pradipta , Chang John T. , Chu Hiutung , Dorrestein Pieter , Zhu Qiyun , Chassaing Benoit , Knight Rob , Gonzalez David J. , Dulai Parambir S.
Published: January 2022

Objective

This study examined the host-microbe changes underpinning treatment response to hyperbaric oxygen therapy (HBOT) in ulcerative colitis.

Design

Pre- and post-intervention mucosal tissue and fecal samples from two clinical trials, along with fecal samples from healthy controls and fecal and mucosal tissue from disease severity matched UC controls. Mucosal tissue bulk-RNA sequencing, digital spatial profiling (DSP) for single-cell RNA and protein analysis, and immunohistochemistry was performed, in addition to 16S rRNA, shotgun metagenomics, metabolomics, and metaproteomics of fecal samples. Fecal colonization experiments in IL10-/- germ-free mice were performed to confirm observations.

Results

Proteomics identified associations between HBOT response status and neutrophil degranulation, with specificity of effect for azurophilic granules. DSP identified a specific HBOT effect on reducing neutrophil STAT3, which was confirmed by immunohistochemistry. HBOT decreased microbial diversity with an accompanying proportional increase in Firmicutes and a secondary bile acid lithocholic acid. The reduction in diversity was due to reductions in mucinophiles, with differences in Akkermansia muciniphila strains being associated with HBOT response status. Proteomics observed an accompanying effect for HBOT on MUC2. Colonization of IL10-/- with stool obtained from HBOT responders resulted in lower colitis activity compared to stool obtained from HBOT non-responders, with no differences in STAT3 expression, suggesting complementary but independent host and microbial responses.

Conclusion

HBOT reduces host neutrophil STAT3 and azurophilic granule activity in UC patients, and changes in microbial composition and metabolism in ways that improve colitis activity. Intestinal microbiota, especially strain level variations in A. muciniphila, may contribute to HBOT non-response.
Optimized phylogenetic clustering of HIV-1 sequence data for public health applications
Authors: Chato Connor , Feng Yi , Ruan Yuhua , Xing Hui , Herbeck Joshua , Kalish Marcia , Poon Art F. Y.
Published: January 2022

Clusters of genetically similar infections suggest rapid transmission and may indicate priorities for public health action or reveal underlying epidemiological processes. However, clusters often require user-defined thresholds and are sensitive to non-epidemiological factors, such as non-random sampling. Consequently the ideal threshold for public health applications varies substantially across settings. Here, we show a method which selects optimal thresholds for phylogenetic (subset tree) clustering based on population. We evaluated this method on HIV-1 pol datasets (n = 14,221 sequences) from four sites in USA (Tennessee, Seattle), Canada (Northern Alberta) and China (Beijing). Clusters were defined by tips descending from an ancestral node (with a minimum bootstrap support of 95%) through a series of branches, each with a length below a given threshold. Next, we used pplacer to graft new cases to the fixed tree by maximum likelihood. We evaluated the effect of varying branch-length thresholds on cluster growth as a count outcome by fitting two Poisson regression models: a null model that predicts growth from cluster size, and an alternative model that includes mean collection date as an additional covariate. The alternative model was favoured by AIC across most thresholds, with optimal (greatest difference in AIC) thresholds ranging 0.007–0.013 across sites. The range of optimal thresholds was more variable when re-sampling 80% of the data by location (IQR 0.008 – 0.016, n = 100 replicates). Our results use prospective phylogenetic cluster growth and suggest that there is more variation in effective thresholds for public health than those typically used in clustering studies.
The secreted metabolome of HeLa cells under effect of Crotamine, a cell-penetrating peptide from a rattlesnake using NMR-based metabolomics analyses
Authors: Coronado Monika Aparecida , de Moraes Fábio Rogério , Stuqui Bruna , Calmon Marília Freitas , Eberle Raphael Josef , Rahal Paula , Arni Raghuvir Krishnaswamy
Published: January 2022

Sequestering and reprogramming of cellular metabolism represents one of the principal hallmarks several cells. Antimicrobial peptides have been shown to exhibit selective anticancer activities. In this study, the secreted metabolome of HeLa cells under action of the antimicrobial peptide Crotamine was evaluated. Although, Crotamine has been shown to be selective for highly proliferating cells and is able to extend the in vivo lifespan. The present study using a cell line of cervical cancer, HeLa cells provide insights into how Crotamine acts in cell metabolism. NMR spectroscopy was used to identify and quantify relative metabolite levels, which are associated with Crotamine uptake. Statistical analysis reveals that Crotamine dramatically affects metabolites related to glycolysis, metabolism and biosynthesis of amino acids and pyruvate metabolism. The developed machine learning model is found to be robust by ROC curve analysis, suggesting that the metabolic state of HeLa cells treated with Crotamine is different from the control samples. To account for metabolite levels, it is suggested that Crotamine would have to act on glycolysis, which, in turn, affects several other metabolic pathways, such as, glutathione metabolism, TCA cycle and pyruvate metabolism. The observed metabolic changes shed light into the mode of Crotamine function.
Engineering Rotating Apical-Out Airway Organoid for Assessing Respiratory Cilia Motility
Authors: Wijesekara Piyumi , Yadav Prakarsh , Perkins Lydia A. , Stolz Donna B. , Franks Jonathan M. , Watkins Simon C. , Jacome Emily Reinoso , Brody Steven L. , Horani Amjad , Xu Jian , Farimani Amir Barati , Ren Xi
Published: January 2022

Motile cilia project from the airway apical surface and directly interface with inhaled external environment. Due to cilia’s nanoscale dimension and high beating frequency, quantitative assessment of their motility remains a sophisticated task. Here we described a robust approach for reproducible engineering of apical-out airway organoid (AOAO) of defined size. Propelled by exterior-facing cilia beating, the mature AOAO exhibited stable rotational motion when surrounded by Matrigel. We developed a computational framework leveraging computer vision algorithms to quantify AOAO rotation and validated its correlation with direct measurement of cilia motility. We further established the feasibility of using AOAO rotation to recapitulate and measure defective cilia motility caused by chemotherapy-induced toxicity and by CCDC39 mutations in cells from primary ciliary dyskinesia patient. We expect our rotating AOAO model and the associated computational pipeline to offer a generalizable framework to expediate modeling of and therapeutic development for genetic and environmental ciliopathies.
MERIT: controlling Monte-Carlo error rate in large-scale Monte-Carlo hypothesis testing
Authors: Li Yunxiao , Hu Yi-Juan , Satten Glen A.
Published: January 2022

The use of Monte-Carlo (MC) p-values when testing the significance of a large number of hypotheses is now commonplace. In large-scale hypothesis testing, we will typically encounter at least some p-values near the threshold of significance, which require a larger number of MC replicates than p-values that are far from the threshold. As a result, the list of detections can vary when different MC replicates are used, resulting in lack of reproducibility. The method of Gandy and Hahn (GH) (2014; 2016; 2017) is the only method that has directly addressed this problem, defining a Monte-Carlo error rate (MCER) to be the probability that any decisions on accepting or rejecting a hypothesis based on MC p-values are different from decisions based on ideal p-values, and then making decisions that control the MCER. Unfortunately, GH is frequently very conservative, often making no rejections at all and leaving a large number of hypotheses “undecided”. In this article, we propose MERIT, a method for large-scale MC hypothesis testing that also controls the MCER but is more statistically efficient than the GH method. Through extensive simulation studies, we demonstrated that MERIT controlled the MCER and substantially improved the sensitivity and specificity of detections compared to GH. We also illustrated our method by an analysis of gene expression data from a prostate cancer study.
Rapid and repeatable genome evolution across three hybrid ant populations
Authors: Nouhaud Pierre , Martin Simon H. , Portinha Beatriz , Sousa Vitor C. , Kulmuni Jonna
Published: January 2022

Hybridization is frequent in the wild but it is unclear whether admixture events lead to predictable outcomes and if so, at what timescale. We show that selection led to correlated sorting of genetic variation in less than 50 generations in three hybrid Formica aquilonia × F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened repeatedly in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.
Strategies of invertebrate osmoregulation: an evolutionary blueprint for transmuting into fresh water from the sea
Authors: McNamara John Campbell , Freire Carolina Arruda
Published: January 2022

Early marine invertebrates like the Branchiopoda began their sojourn into dilute media some 500 million years ago in the Middle Cambrian. Others like the Mollusca, Annelida and many crustacean taxa have followed, accompanying major marine transgressions and regressions, shifting landmasses, orogenies and glaciations. In adapting to these events and new habitats such invertebrates acquired novel physiological abilities that attenuate the ion loss and water gain that constitute severe challenges to life in dilute media. Among these taxon-specific adaptations, selected from the subcellular to organismal levels of organization, are reduced body permeability and surface (S) to volume (V) ratios, lowered osmotic gradients, increased surface areas of interface epithelia, relocation of membrane proteins in ion-transporting cells and augmented transport enzyme abundance, activity and affinity. We examine adaptations in taxa that have penetrated into fresh water, revealing diversified modifications, a consequence of distinct body plans, morpho-physiological resources and occupation routes. Contingent on life history and reproductive strategy, numerous patterns of osmotic regulation have emerged, including intracellular isosmotic regulation in weak hyper-regulators and well-developed anisosmotic extracellular regulation in strong hyper-regulators, likely reflecting inertial adaptations to early life in an estuarine environment. Our analyses show that across sixty-four freshwater invertebrate species from six phyla/classes, hemolymph osmolalities decrease logarithmically with increasing S: V ratios. The arthropods have the highest osmolalities, from 300 to 650 mOsmoles/kg H2O in the Decapoda with 220 to 320 mOsmoles/kg H2O in the Insecta; osmolalities in the Annelida range from 150 to 200 mOsmoles/kg H2O, the Mollusca showing the lowest osmolalities at 40 to 120 mOsmoles/kg H2O. Overall, osmolalities reach a cut-off at ≈200 mOsmoles/kg H2O, independently of increasing S: V ratio. The ability of species with small S: V ratios to maintain large osmotic gradients is mirrored in their putatively higher Na+/K+-ATPase activities that drive ion uptake processes. Selection pressures on these morpho-physiological characteristics have led to differential osmoregulatory abilities, rendering possible the conquest of fresh water while retaining some tolerance of the ancestral medium.
Novel MBLs inhibitors screened from FDA-approved drug library restore the susceptibility of carbapenems to NDM-1-harbouring bacteria
Authors: Guo Yan , Liu Hongtao , Yang Mengge , Ding Rui , Gao Yawen , Niu Xiaodi , Deng Xuming , Wang Jianfeng , Feng Haihua , Qiu Jiazhang
Published: January 2022

The production of metallo-β-lactamases (MBLs) is one of the major mechanisms adopted by bacterial pathogens to resist carbapenems. One promising strategy to overcome MBLs-mediated carbapenems resistance is to develop effective inhibitors. Repurposing approved drugs to restore the efficacy of carbapenems represents an efficient and cost-effective approach to fight infections caused by carbapenem resistant pathogens. Here, twelve FDA-approved compounds were screened to neutralize the ability of NDM-1. Among these compounds, dexrazoxane, embelin, candesartan cilexetil (CAN) and nordihydroguaiaretic acid (NDGA) were further demonstrated to inhibit all tested MBLs, and showed an in vitro synergistic bactericidal effect with meropenem against MBLs-producing bacteria. Mechanistic studies revealed that dexrazoxane, embelin and CAN are metal ion chelating agents, while the inhibition of NDM-1 by NDGA involves its direct binding with the active region of NDM-1. Furthermore, dexrazoxane, embelin and CAN and NDGA dramatically rescued the treatment efficacy of meropenem in three infection models. Our observations indicated that dexrazoxane, embelin, CAN and NDGA are promising carbapenem adjuvants against MBLs-positive carbapenem resistant bacterial pathogens.
Rapid exchange of stably bound protein and DNA cargo on a DNA origami receptor
Authors: Brown James W.P. , Alford Rokiah G. , Walsh James C. , Spinney Richard E. , Xu Stephanie Y. , Hertel Sophie , Berengut Jonathan F. , Spenkelink Lisanne M. , van Oijen Antoine M. , Böcking Till , Morris Richard G. , Lee Lawrence K.
Published: January 2022

Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multi-valent interactions to form stable complexes that are simultaneously capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multi-site competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo; an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to be the first of many that use DNA origami structures to exploit multi-valent interactions for the design and synthesis of a wide range of possible kinetic behaviors.
Light activation of Orange Carotenoid Protein reveals bicycle-pedal single-bond isomerization
Authors: Chukhutsina V.U. , Baxter J.M. , Fadini A. , Morgan R.M. , Pope M.A. , Maghlaoui K. , Orr C.M. , Wagner A. , van Thor J.J.
Published: January 2022

Orange Carotenoid protein (OCP) is the only known photoreceptor which uses carotenoid for its activation. It is found exclusively in cyanobacteria, where it functions to control light-harvesting of the photosynthetic machinery. However, the photochemical reactions and structural dynamics of this unique photosensing process are not yet resolved. We present time-resolved crystal structures at second-to-minute delays under bright illumination, capturing the early photoproduct and structures of the subsequent reaction intermediates. The first stable photoproduct shows concerted isomerization of C9’-C8’ and C7’-C6’ single bonds in the bicycle-pedal (BP) manner and structural changes in the N-terminal domain with minute timescale kinetics. These are followed by a thermally-driven recovery of the BP isomer to the dark state carotenoid configuration. Structural changes propagate to the C-terminal domain, resulting, at later time, in the H-bond rupture of the carotenoid keto group with protein residues. The isomerization and its transient nature are confirmed in OCP crystals and solution by FTIR and UV/Vis spectroscopy. This study reveals the single bond isomerization of the carotenoid in the BP manner and subsequent thermal structural reactions as the basis of OCP photoreception. Understanding and potentially controlling the OCP dynamics offers the prospect of novel applications in biomass engineering as well as in optogenetics and bioimaging.
A hippocampal-hypothalamic circuit essential for anxiety-related behavioral avoidance
Authors: Yan Jing-Jing , Chen Ai-Xiao , Zhang Wen , He Ting , Ding Xiao-Jing , Yu Zi-Xian , Zhang Yan-Li , He Mengge , Li Haohong , Xu Xiao-Hong
Published: January 2022

Anxiety over perceived threats triggers avoidance behavior, but the underlying neural circuit mechanism remains poorly understood. Taking hints from the deep connection between anxiety and predator defense, we examined the role of the anterior hypothalamic nucleus (AHN), a critical node in the predator defense network, in anxiety-related behaviors. By recording Ca2+ transients in behaving mice, we found that activity of AHN GABAergic (AHNVgat+) neurons showed individually stable increases when animals approached unfamiliar objects in an open field (OF) or explored the open arm of an elevated plus-maze (EPM). Moreover, AHNVgat+ neuron activity foreshadowed behavioral retreats and correlated with object and open-arm avoidance. Crucially, exploration-triggered optogenetic inhibition of AHNVgat+ neurons dramatically reduced avoidance behaviors. Furthermore, retrograde viral tracing identified the ventral subiculum (vSub) of the hippocampal formation as a significant input to AHNVgat+ neurons in driving avoidance behaviors. Thus, the activity of the hippocampal-hypothalamic pathway promotes idiosyncratic anxiety-related behavioral avoidance.
Thermodynamic analysis of Zα domain-nucleic acid interactions
Authors: Srinivasan Bharath , Kuś Krzysztof , Athanasiadis Alekos
Published: January 2022

DNA/RNA molecules adopting the left-handed conformation (Z-form) have been attributed with immunogenic properties. However, their biological role and importance has been a topic of debate for many years. The discovery of Z-DNA/RNA binding domains (Zα domains) in varied proteins that are involved in the innate immune response, such as the interferon inducible form of the RNA editing enzyme ADAR1 (p150), Z-DNA binding protein 1 (ZBP1), the fish kinase PKZ and the poxvirus inhibitor of interferon response E3L, indicates important roles of Z-DNA/RNA in immunity and self/non-self-discrimination. Such Zα domain-containing proteins recognise left-handed Z-DNA/RNA in a conformation-specific manner. Recent studies have implicated these domains in virus recognition. Given these important emerging roles for the Zα domains, it is pivotal to understand the mechanism of recognition of the Z-DNA/Z-RNA by these domains. To this end, we assessed the binding thermodynamics of Zα domain from ORF112 and ADAR1 on T(CG)3 and T(CG)6 oligonucleotides which have high propensity to adopt the Z-conformation. Our study highlights important differences in the mode of binding by the two Zα domains originating from different proteins. Site-directed mutagenesis was employed together with isothermal titration calorimetry to tease apart finer details of the binding thermodynamics. Our work advances the understanding on binding thermodynamics of Zα domains to their cognate nucleic acid substrates and contributes to the efforts to gain a complete appreciation of this process.
The asymmetric distribution of RNA polymerase II and nucleosomes on replicated daughter genomes is caused by differences in replication timing between the lagging and the leading strand
Authors: Ziane Rahima , Camasses Alain , Radman-Livaja Marta
Published: January 2022

Chromatin features are thought to have a role in the epigenetic transmission of transcription states from one cell generation to the next. It is unclear how chromatin structure survives disruptions caused by genomic replication or whether chromatin features are instructive of the transcription state of the underlying gene. We developed a method to monitor budding yeast replication, transcription, and chromatin maturation dynamics on each daughter genome in parallel, with which we identified clusters of secondary origins surrounding known origins. We found a difference in the timing of lagging and leading strand replication on the order of minutes at most yeast genes. We propose a model in which the majority of old histones and RNA polymerase II (RNAPII) bind to the gene copy that replicated first, while newly synthesized nucleosomes are assembled on the copy that replicated second. RNAPII enrichment then shifts to the sister copy that replicated second. The order of replication is largely determined by genic orientation: If transcription and replication are codirectional, the leading strand replicates first; if they are counterdirectional, the lagging strand replicates first. A mutation in the Mcm2 subunit of the replicative helicase Mcm2-7 that impairs Mcm2 interactions with histone H3 slows down replication forks but does not qualitatively change the asymmetry in nucleosome distribution observed in the WT. We propose that active transcription states are inherited simultaneously and independently of their underlying chromatin states through the recycling of the transcription machinery and old histones, respectively. Transcription thus actively contributes to the reestablishment of the active chromatin state.
Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
Authors: Gupta Anushka , Shamsi Farnaz , Altemose Nicolas , Dorlhiac Gabriel F. , Cypess Aaron M. , White Andrew P. , Yosef Nir , Patti Mary Elizabeth , Tseng Yu-Hua , Streets Aaron
Published: January 2022

Single-cell RNA sequencing (scRNA-seq) enables molecular characterization of complex biological tissues at high resolution. The requirement of single-cell extraction, however, makes it challenging for profiling tissues such as adipose tissue, for which collection of intact single adipocytes is complicated by their fragile nature. For such tissues, single-nucleus extraction is often much more efficient and therefore single-nucleus RNA sequencing (snRNA-seq) presents an alternative to scRNA-seq. However, nuclear transcripts represent only a fraction of the transcriptome in a single cell, with snRNA-seq marked with inherent transcript enrichment and detection biases. Therefore, snRNA-seq may be inadequate for mapping important transcriptional signatures in adipose tissue. In this study, we compare the transcriptomic landscape of single nuclei isolated from preadipocytes and mature adipocytes across human white and brown adipocyte lineages, with whole-cell transcriptome. We show that snRNA-seq is capable of identifying the broad cell types present in scRNA-seq at all states of adipogenesis. However, we also explore how and why the nuclear transcriptome is biased and limited, as well as how it can be advantageous. We robustly characterize the enrichment of nuclear-localized transcripts and adipogenic regulatory lncRNAs in snRNA-seq, while also providing a detailed understanding for the preferential detection of long genes upon using this technique. To remove such technical detection biases, we propose a normalization strategy for a more accurate comparison of nuclear and cellular data. Finally, we show successful integration of scRNA-seq and snRNA-seq data sets with existing bioinformatic tools. Overall, our results illustrate the applicability of snRNA-seq for the characterization of cellular diversity in the adipose tissue.
Behavioral and neural mechanisms of latent inhibition
Authors: Miller Dylan B. , Rassaby Madeleine M. , Collins Katherine A. , Milad Mohammad R.
Published: January 2022

Fear is an adaptive emotion that serves to protect an organism against potential dangers. It is often studied using classical conditioning paradigms where a conditioned stimulus is paired with an aversive unconditioned stimulus to induce a threat response. Less commonly studied is a phenomenon that is related to this form of conditioning, known as latent inhibition. Latent inhibition (LI) is a paradigm in which a neutral cue is repeatedly presented in the absence of any aversive associations. Subsequent pairing of this pre-exposed cue with an aversive stimulus typically leads to reduced expression of a conditioned fear/threat response. In this article, we review some of the theoretical basis for LI and its behavioral and neural mechanisms. We compare and contrast LI and fear/threat extinction—a process in which a previously conditioned cue is repeatedly presented in the absence of aversive outcomes. We end with highlighting the potential clinical utility of LI. Particularly, we focus on how LI application could be useful for enhancing resilience, especially for individuals who are more prone to continuous exposure to trauma and stressful environments, such as healthcare workers and first responders. The knowledge to be gained from advancing our understanding of neural mechanisms in latent inhibition could be applicable across psychiatric disorders characterized by exaggerated fear responses and impaired emotion regulation.