bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolomics reveals the within-plant spatial effects of shading on tea plants
Authors: Zhang Qunfeng , Liu Meiya , Mumm Roland , Vos Ric C H , Ruan Jianyun
Published: October 2020

It is well known that green tea made from fully developed leaves located at the base of young shoots is of lower quality than that made from the still developing leaves located on the top of the shoot. It has additionally been shown that plant shading can significantly improve green tea quality. Here, we aimed to get more insight into the effects of shading on the overall metabolome in different parts of the tea shoots. To do this, field-grown tea plants were shaded by coverage with either a straw layer or a black net, both blocking the daylight intensity for more than 90%. Both the first (i.e. still developing) leaf and the fourth (i.e. fully developed) leaf, as well as the stem of young shoots were harvested and subjected to complementary untargeted metabolomics approaches, using accurate mass LC-Orbitrap-Fourier transform mass spectrometry (FTMS) for profiling both semi-polar and lipid-soluble compounds and GC-TOF-MS for profiling polar compounds. In total, 1419 metabolites were detected. Shading resulted in a decreased ratio of polyphenols to amino acids (which improves the quality of green tea) and lower levels of galloylated catechins in the shoots. The positive effect of shading on the amino acid/catechin ratio was more pronounced in the fully developed (fourth) than in the developing (first) leaves. Furthermore, many metabolites, especially organic acids, carbohydrates and amino acids, showed differential or opposite responses to the shading treatments between the three shoot tissues investigated, suggesting a within-plant spatial regulation or transport/redistribution of carbon and nitrogen resources between the tissues of the growing young shoots. This work provides new insight into the spatial effects of shading on tea plants, which could further help to increase tea quality by improving cultivation measures for plant shading.

Highlights
Genome Sequence Resource for Colletotrichum scovillei, the Cause of Anthracnose Disease of Chili
Authors: Huo Jianfei , Wang Yafei , Hao Yongjuan , Yao Yurong , Wang Yong , Zhang Kai , Tan Xinqiu , Li Zhiqiang , Wang Wanli
Published: October 2020

Colletotrichum species cause anthracnose disease on the economically important spice crop chili. A total of 24 Colletotrichum species are known to infect chili and cause anthracnose. C. scovillei belongs to the C. acutatum species complex, and it shows greater aggressiveness than other species, particularly in the case of inoculation onto the nonwounded fruits of chili plants. The current work introduces an initial Illumina-Nanopore hybrid draft genome for C. scovillei TJNH1 together with the related annotations. Knowledge of this genome sequence provides an important reference genome of C. scovillei and will help further understand the pathogenic mechanism of C. scovillei to plant.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Transcriptome Analysis of the Grape-Elsinoë ampelina Pathosystem Reveals Novel Effectors and a Robust Defense Response
Authors: Li Zhi , Wang Ya , Fan Yanchun , Ahmad Bilal , Wang Xianhang , Zhang Songlin , Zhu Yanxun , Gao Linlin , Chang Pingping , Wang Xiping
Published: October 2020

Elsinoë ampelina is an ascomycetous fungus that causes grape anthracnose, a potentially devastating disease worldwide. In this study, a dual RNA-seq analysis was used to simultaneously monitor the fungal genes related to pathogenesis and grape genes related to defense during the interaction at 2, 3, 4, and 5 days postinoculation. Consistent with their potential roles in pathogenicity, genes for carbohydrate-active enzymes, secondary metabolite synthesis, pathogen-host interaction, and those encoding secreted proteins are upregulated during infection. Based on Agrobacterium tumefaciens–mediated transient assays in Nicotiana benthamiana, we further showed that eight and nine candidate effectors, respectively, suppressed BAX- and INF1-mediated programmed cell death. The host response was characterized by the induction of multiple defense systems against E. ampelina, including synthesis of phenylpropanoids, stilbenes, and terpenoid biosynthesis, cell-wall modifications, regulation by phytohormones, and expression of defense-related genes. Together, these findings offer new insights into molecular mechanisms underlying the grape–E. ampelina interaction.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Low Spontaneous Breathing Effort during Extracorporeal Membrane Oxygenation in a Porcine Model of Severe Acute Respiratory Distress Syndrome
Authors: Dubo Sebastián , Oviedo Vanesa , Garcia Alinee , Alegría Leyla , García Patricio , Valenzuela Emilio Daniel , Damiani L. Felipe , Araos Joaquín , Medina Tania , Bachmann María Consuelo , Basoalto Roque , Bravo Sebastián , Soto Dagoberto , Cruces Pablo , Guzmán Pablo , Retamal Jaime , Cornejo Rodrigo , Bugedo Guillermo , Brebi Priscilla , Bruhn Alejandro
Published: October 2020

Background

A lung rest strategy is recommended during extracorporeal membrane oxygenation in severe acute respiratory distress syndrome (ARDS). However, spontaneous breathing modes are frequently used in this context. The impact of this approach may depend on the intensity of breathing efforts. The authors aimed to determine whether a low spontaneous breathing effort strategy increases lung injury, compared to a controlled near-apneic ventilation, in a porcine severe ARDS model assisted by extracorporeal membrane oxygenation.

Methods

Twelve female pigs were subjected to lung injury by repeated lavages, followed by 2-h injurious ventilation. Thereafter, animals were connected to venovenous extracorporeal membrane oxygenation and during the first 3 h, ventilated with near-apneic ventilation (positive end-expiratory pressure, 10 cm H2O; driving pressure, 10 cm H2O; respiratory rate, 5/min). Then, animals were allocated into (1) near-apneic ventilation, which continued with the previous ventilatory settings; and (2) spontaneous breathing: neuromuscular blockers were stopped, sweep gas flow was decreased until regaining spontaneous efforts, and ventilation was switched to pressure support mode (pressure support, 10 cm H2O; positive end-expiratory pressure, 10 cm H2O). In both groups, sweep gas flow was adjusted to keep Paco
2 between 30 and 50 mmHg. Respiratory and hemodynamic as well as electric impedance tomography data were collected. After 24 h, animals were euthanized and lungs extracted for histologic tissue analysis.

Results

Compared to near-apneic group, the spontaneous breathing group exhibited a higher respiratory rate (52 ± 17 vs. 5 ± 0 breaths/min; mean difference, 47; 95% CI, 34 to 59; P < 0.001), but similar tidal volume (2.3 ± 0.8 vs. 2.8 ± 0.4 ml/kg; mean difference, 0.6; 95% CI, –0.4 to 1.4; P = 0.983). Extracorporeal membrane oxygenation settings and gas exchange were similar between groups. Dorsal ventilation was higher in the spontaneous breathing group. No differences were observed regarding histologic lung injury.

Conclusions

In an animal model of severe ARDS supported with extracorporeal membrane oxygenation, spontaneous breathing characterized by low-intensity efforts, high respiratory rates, and very low tidal volumes did not result in increased lung injury compared to controlled near-apneic ventilation.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
Perioperative Opioid Administration
Authors: Shanthanna Harsha , Ladha Karim S. , Kehlet Henrik , Joshi Girish P.
Published: October 2020

Opioids form an important component of general anesthesia and perioperative analgesia. Discharge opioid prescriptions are identified as a contributor for persistent opioid use and diversion. In parallel, there is increased enthusiasm to advocate opioid-free strategies, which include a combination of known analgesics and adjuvants, many of which are in the form of continuous infusions. This article critically reviews perioperative opioid use, especially in view of opioid-sparing versus opioid-free strategies. The data indicate that opioid-free strategies, however noble in their cause, do not fully acknowledge the limitations and gaps within the existing evidence and clinical practice considerations. Moreover, they do not allow analgesic titration based on patient needs; are unclear about optimal components and their role in different surgical settings and perioperative phases; and do not serve to decrease the risk of persistent opioid use, thereby distracting us from optimizing pain and minimizing realistic long-term harms.
Genetic variations of three important antioxidative enzymes SOD2, CAT, and GPX1 in nonalcoholic steatohepatitis
Authors: Huang Yi-Shin , Chang Tien-En , Perng Chin-Lin , Huang Yi-Hsiang
Published: October 2020

Background:

Nonalcoholic steatohepatitis (NASH) is closely related to reactive oxygen species (ROS). Superoxide anion radicals, the main product of ROS, can be reduced by manganese superoxide dismutase (SOD2) to hydrogen peroxide, which is further reduced by catalase (CAT) and glutathione peroxidase (GPX) to water. We aimed to investigate the association between the most important genetic variants of SOD2, CAT, and GPX1 and susceptibility to NASH.

Methods:

A total of 126 adults with liver tissue-verified NASH, 56 patients with liver tissue-verified nonalcoholic fatty liver (NAFL), and 153 healthy controls were enrolled. Their DNA profiles were retrieved for genotype assessment of SOD2 47T>C (rs4880), CAT -262C>T (rs1001179), and GPX1 593C>T (rs1050450) variation.

Results:

There were statistical differences between the SOD2 and CAT genotypes across the NASH, NAFL, and control groups, but not GPX1. The NASH group had a significantly higher frequency of subjects with SOD2 C allele (38.8%) compared with the NASL group (25.0%) and the controls (22.9%, p = 0.010). Similarly, the NASH group had a significantly higher percentage of subjects with CAT T allele (23.0%) compared with the NAFL group (10.7%) and the controls (7.2%, p = 0.001). For subjects with both the SOD2 C allele and CAT T allele, 88.2% were in the NASH group. After adjusting for confounders, the CAT mutant T allele and SOD2 mutant C allele were still the highest independent risk factors for NASH (odds ratio [OR] 3.10 and 2.36, respectively). In addition, there was a synergistic effect for those two alleles and the occurrence of NASH with an adjusted OR of 8.57 (p = 0.030).

Conclusion:

The genetic variations of CAT and SOD2 may increase the risk of NASH, which may aid in the screening of patients who are at high risk of NASH, and offer a potential anti-oxidant targeting route for the treatment of NASH.
Risk factors of strabismus surgery among pediatric cerebral palsy population with strabismus in Taiwan: A population-based cohort study
Authors: Lai Wei-Yu , Kuo Tsu-Jen , Lee Ching-Chih , Yin Chun-Hao
Published: October 2020

Background:

To identify the risk factors of strabismus surgery among Taiwanese children with severe cerebral palsy (CP) and strabismus.

Methods:

This retrospective nationwide population-based cohort study examined a cohort of newly diagnosed pediatric CP patients (age ≤ 10 y) between 1997 and 2013 with strabismus. The primary endpoint was strabismus surgery. A stepwise logistic regression was applied to determine the demographic factors, ophthalmic conditions, and comorbidities associated with strabismus surgery.

Results:

Out of 808 patients, 115 had received strabismus surgery. The significant factors correlated to strabismus surgery in pediatric patients with severe CP and strabismus were CP diagnosis age < 4 years, residency in a suburban/rural area, low birth weight, and strabismic amblyopia.

Conclusion:

In CP children with strabismus who have risk factors of younger CP diagnosis age (age < 4 y), residency in a suburban/rural area, a low birthweight, and the presence of strabismic amblyopia, strabismus surgery should be considered.
Variants of significance: medical genetics and surgical outcomes in congenital heart disease
Authors: Geddes Gabrielle C. , Przybylowski Leon F. , Ware Stephanie M.
Published: October 2020

Purpose of review

This article reviews the current understanding and limitations in knowledge of the effect genetics and genetic diagnoses have on perioperative and postoperative surgical outcomes in patients with congenital heart disease (CHD).

Recent findings

Presence of a known genetic diagnosis seems to effect multiple significant outcome metrics in CHD surgery including length of stay, need for extracorporeal membrane oxygenation, mortality, bleeding, and heart failure. Data regarding the effects of genetics in CHD is complicated by lack of standard genetic assessment resulting in inaccurate risk stratification of patients when analyzing data. Only 30% of variation in CHD surgical outcomes are explained by currently measured variables, with 2.5% being attributed to diagnosed genetic disorders, it is thought a significant amount of the remaining outcome variation is because of unmeasured genetic factors.

Genetic diagnoses clearly have a significant effect on surgical outcomes in patients with CHD. Our current understanding is limited by lack of consistent genetic evaluation and assessment as well as evolving knowledge and discovery regarding the genetics of CHD. Standardizing genetic assessment of patients with CHD will allow for the best risk stratification and ultimate understanding of these effects.
Characteristics of Upper Extremity Recovery in Acute Flaccid Myelitis: A Case Series
Authors: Weber Erin L. , Werner Julie M. , Johnson Maxwell B. , Kim Gina , Tiongson Emmanuelle , Ramos-Platt Leigh , Seruya Mitchel
Published: October 2020

Background:

Clinical characteristics and timing associated with nonsurgical recovery of upper extremity function in acute flaccid myelitis are unknown.

Methods:

A single-institution retrospective case series was analyzed to describe clinical features of acute flaccid myelitis diagnosed between October of 2013 and December of 2016. Patients were consecutively sampled children with a diagnosis of acute flaccid myelitis who were referred to a hand surgeon. Patient factors and initial severity of paralysis were compared with upper extremity muscle strength outcomes using the Medical Research Council scale every 3 months up to 18 months after onset.

Results:

Twenty-two patients with acute flaccid myelitis (aged 2 to 16 years) were studied. Proximal upper extremity musculature was more frequently and severely affected, with 56 percent of patients affected bilaterally. Functional recovery of all muscle groups (≥M3) in an individual limb was observed in 43 percent of upper extremities within 3 months. Additional complete limb recovery to greater than or equal to M3 after 3 months was rarely observed. Extraplexal paralysis, including spinal accessory (72 percent), glossopharyngeal/hypoglossal (28 percent), lower extremity (28 percent), facial (22 percent), and phrenic nerves (17 percent), was correlated with greater severity of upper extremity paralysis and decreased spontaneous recovery. There was no correlation between severity of paralysis or recovery and patient characteristics, including age, sex, comorbidities, prodromal symptoms, or time to paralysis.

Conclusions:

Spontaneous functional limb recovery, if present, occurred early, within 3 months of the onset of paralysis. The authors recommend that patients without signs of early recovery warrant consideration for early surgical intervention and referral to a hand surgeon or other specialist in peripheral nerve injury.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Risk, III.
A Retrospective, Matched Case-Control Study on the Risk Factors of Falls and Varying Severities of Fall-Related Injuries in Inpatients
Authors: Chang Wen-Pei , Jen Hsiu-Ju
Published: October 2020

Objective

This study was to investigate the factors that influence falls and the severity of fall-related injuries in inpatients.

Methods

We adopted a retrospective, matched case-control design and conducted this study at a teaching hospital in Taiwan. Our study period ran from January 2016 to December 2019. We searched for inpatients with official fall records and obtained data from 823 patients, and then established a control group comprising 331 matching patients based on age, sex, length of hospital stay at time of fall incident, and ward type, thereby resulting in 1154 patients in all. A cumulative logistic regression model was applied to the data collected from medical records and fall incident reports to identify the factors that influence falls and the severity of fall-related injuries in inpatients.

Results

The results indicated that the use of sedatives (B = 0.49, P < 0.001), impaired consciousness (B = 0.64, P < 0.001), normal weight versus obese (B = −0.59, P = 0.008), low hemoglobin levels (B = −0.08, P = 0.003), an unsteady gait versus a normal gait (B = 1.82, P < 0.001), and history of falling within the past year (B = 0.56, P < 0.001) were correlated with the falls and the severity of fall-related injuries.

Conclusions

Our results indicate that the use of sedatives, impaired consciousness, obesity, low hemoglobin levels, poor gait function, and history of falling within the past year are all independent factors that influence falls and the severity of fall-related injuries. This study can provide medical personnel with a reference for the identification of patients with a high risk of falling and implementation of fall prevention measures.
A Study on the Status and Contributory Factors of Adverse Events Due to Negligence in Nursing Care
Authors: Kim Min Ji , Jang Seung Gyeong , Kim In Sook , Lee Won
Published: October 2020

Background

Patient safety issues in medical institutions have received worldwide attention. Nurses play a pivotal role in providing health care at the bedside and the interception of adverse events (AEs). A knowledge of contributory factors for these AEs is vital to individuals, institutional procedures, and also national policy. The goals of this study are to analyze medical litigation related to nursing practice and to determine the most common contributory factors of AEs due to negligence in nursing care.

Methods

A qualitative content analysis was conducted for AEs related to nursing care to determine the general characteristics and contributory factors. The contributory factors for each case were examined using a modified version of the Yorkshire Contributory Factors Framework.

Results

The most common types of AEs in nursing involved surgeries, procedures/interventions, and medications. The analysis also revealed that situational factors and communication and culture factors contributed most to AEs. Individual staff factors and staff training and education were the most frequent subfactors contributing to AEs.

Conclusions

Adverse events were associated with various contributory factors that varied according to AE type. Thus, strategies need to be developed based on the understanding of these contributory factors related to the different AE types so that comprehensive approaches to improving patient safety and quality of nursing care can be implemented.
The infant pharyngeal microbiomes: origin, impact and manipulation
Authors: Theodosiou Anastasia A. , Dorey Robert B. , Read Robert C. , Jones Christine E.
Published: October 2020

Purpose of review

There has been an exponential increase in research into infant microbiome evolution, and it appears that pharyngeal microbiota are associated with clinical phenotypes (e.g. infection and asthma). Although broad consensus views are emerging, significant challenges and uncertainties remain.

Recent findings

Infant pharyngeal microbiome research is limited by low biomass, high temporal diversity and lack of agreed standards for sampling, DNA sequencing and taxonomic reporting. Analysis of amplicon sequence variants and improved cost and availability of whole-genome sequencing are promising options for improving taxonomic resolution of such studies. Infant respiratory microbiomes arise, at least in part, from maternal flora (e.g. the respiratory tract and breastmilk), and are associated with environmental and clinical factors (e.g. mode of feeding and delivery, siblings, daycare attendance, birth season and antibiotic usage). Interventional research to modify the infant pharyngeal microbiota has recently been reported, using dietary supplements.

Further work is needed to improve characterization of the infant pharyngeal microbiomes, including routes of bacterial acquisition, role of environmental factors and associations with disease phenotypes. Methodological standards are desirable to facilitate more reproducible, comparable research. Improved understanding may enable manipulation of infant pharyngeal microbiota to improve clinical outcomes.
Automated Analysis of Medial Gastrocnemius Muscle-Tendon Junction Displacements During Isolated Contractions and Walking Using Deep Neural Networks
Authors: Krupenevich Rebecca L. , Funk Callum J. , Franz Jason R.
Published: October 2020

Direct measurement of muscle-tendon junction (MTJ) position is important for understanding dynamic tendon behavior and muscle-tendon interaction in healthy and pathological populations. Traditionally, obtaining MTJ position during functional activities is accomplished by manually tracking the position of the MTJ in cine B-mode ultrasound images – a laborious and time-consuming process. Recent advances in deep learning have facilitated the availability of user-friendly open-source software packages for automated tracking. However, these software packages were originally intended for animal pose estimation and have not been widely tested on ultrasound images. Therefore, the purpose of this paper was to evaluate the efficacy of deep neural networks to accurately track medial gastrocnemius MTJ positions in cine B-mode ultrasound images across tasks spanning controlled loading during isolated contractions to physiological loading during treadmill walking. Cine B-mode ultrasound images of the medial gastrocnemius MTJ were collected from 15 subjects (6M/9F, 23 yr, 71.9 kg, 1.8 m) during treadmill walking at 1.25 m/s and during maximal voluntary isometric plantarflexor contractions (MVICs). Five deep neural networks were trained using 480 labeled images collected during walking, and were then used to predict MTJ position in images from novel subjects 1) during walking (novel-subject), and 2) during MVICs (novel-condition). We found an average mean absolute error of 1.26±1.30 mm and 2.61±3.31 mm in the novel-subject and novel-condition evaluations, respectively. We believe this approach to MTJ position tracking is an accessible and time-saving solution, with broad applications for many fields, such as rehabilitation or clinical diagnostics.
Engineering supramolecular organizing centers for optogenetic control of innate immune responses
Authors: Tan Peng , He Lian , Zhou Yubin
Published: October 2020

The spatiotemporal organization of oligomeric protein complexes and translocons, such as the supramolecular organizing centers (SMOC) made of MyDDosome and MAVSome, are essential for transcriptional activation of host inflammatory responses and immune metabolisms. Light-inducible assembly of MyDDosome and MAVSome are presented herein to induce activation of nuclear factor-kB (NF-κB) and type-I interferons (IFNs). Engineering of SMOCs and the downstream transcription factor permits programmable and customized innate immune operations in a light-dependent manner. These synthetic molecular tools will likely enable optical and user-defined modulation of innate immunity at a high spatiotemporal resolution to facilitate mechanistic studies of distinct modes of innate immune activations and potential intervention of immune disorders and cancer.
Mitochondrial LonP1 protease is implicated in the degradation of unstable Parkinson disease-associated DJ-1/PARK 7 missense mutants
Authors: Sánchez-Lanzas Raúl , Castaño José G.
Published: October 2020

DJ-1/PARK7mutations are linked with familial forms of early onset Parkinson disease (PD). We have studied the degradation of untagged DJ-1 WT and missense mutants in mouse embryomic fibroblasts obtained from DJ-1 null mice, an approach closer to the situation in patients carrying homozygous mutations. The results showed that the mutants: L10P, M26I, A107P, P158DEL, L166P, E163K and L172Q are unstable proteins, while A39S, E64D, R98Q, A104T, D149A, A171S, K175E and A179T are as stable as the DJ-1 WT. Inhibition of proteasomal and autophagic-lysosomal pathways had little effect on their degradation. Immunofluorescence and biochemical fractionation studies indicated that M26I, A107P, P158DEL, L166P, E163K and L172Q mutants associate with mitochondria. Silencing of mitochondrial matrix protease LonP1 produced a strong reduction of the degradation of those mitochondrialy associated DJ-1 mutants, but not of mutant L10P. These results demonstrated a mitochondrial pathway of degradation of those DJ-1 missense mutants implicated in PD pathogenesis.
Inhibition of Sphingosine-1-Phosphate signaling in pancreatic ductal adenocarcinoma leads to downregulation of growth and invasion
Authors: Rheinheimer Brenna A. , Cardenas Alex , Camacho Luis , Ong Evan S. , Jie Tun , Heimark Ronald L.
Published: October 2020

Background

Deregulated phosphorylation of sphingosine by the sphingosine kinases and signaling through the EDG family of receptors enhances growth and survival in many cell types. Therefore, we sought to elucidate the effect of alterations in the ceramide/sphingosine/S1P rheostat on driving human pancreatic ductal adenocarcinoma towards a malignant phenotype.

Methods

Pancreatic cancer cell lines were treated with exogenous S1P, FTY720, and siRNA to Sphk1. Migration was evaluated by wound healing assays, cell growth by MTT assays, and invasion by tumorsphere assays. Expression of S1PR1, S1PR3, Sphk1, and Sphk2 were measured by quantitative PCR, western blot, and immunohistochemistry.

Results

S1PR1, S1PR3, and Sphk2 were overexpressed in all pancreatic cancer cell lines. Sphk1 translocated from the cytoplasm to the nucleus in cells located at the leading edge of cell clusters. Exogenous S1P increased cell migration while treatment with FTY720 and Sphk1 siRNA decreased cell growth and invasion.

Conclusions

Our results suggest that increased S1PR1 expression may be an early event in pancreatic cancer pathogenesis. Additionally, altered Sphk1 localization may provide a mechanism through which pancreatic ductal adenocarcinoma cells at the leading edge invade into the surrounding matrix. Finally, inhibition of sphingosine-1-phosphate signaling may provide a novel therapeutic target for patients with metastatic disease.
The interplay of HSP90s with YDA regulates main body axis formation during early embryogenesis in Arabidopsis
Authors: Samakovli Despina , Tichá Tereza , Vavrdová Tereza , Závorková Natálie , Pecinka Ales , Ovečka Miroslav , Šamaj Jozef
Published: October 2020

The YODA kinase (YDA) pathway is intimately associated with the control ofArabidopsis thalianaembryo development but little is known regarding its regulators. Using genetic analysis, HEAT SHOCK PROTEINS 90 (HSP90s) emerge as potent regulators of YDA in the process of embryo development and patterning. This study is focused on the characterization and quantification of early embryonal traits of single and doublehsp90andydamutants. The mutant analysis was supported by expression analyses of cell-specificWUSCHEL-RELATED HOMEOBOX2 (WOX2) andWOX8genes during early embryonic development. Chromatin immunoprecipitation assays corroborated the involvement of YDA and HSP90s in the epigenetic control of chromatin remodeling during early embryogenesis. Genetic interactions among HSP90s and members of the YDA signaling pathway affected the development of both embryo proper and suspensor. Impaired function of HSP90s or YDA had an impact on the spatiotemporal expression ofWOX8andWOX2suggesting their essential role in cell fate determination and interference with auxin distribution. Hence, the interplay between HSP90s and YDA signaling cascade mediates the epigenetic control regulating the transcriptional networks shaping early embryo development.
Enhanced Anticoagulation Activity of Functional RNA Origami
Authors: Krissanaprasit Abhichart , Key Carson M. , Froehlich Kristen , Pontula Sahil , Mihalko Emily , Dupont Daniel M. , Andersen Ebbe S. , Kjems Jørgen , Brown Ashley C. , LaBean Thomas H.
Published: October 2020

Anticoagulants are commonly utilized during surgeries and to treat thrombotic diseases like stroke and deep vein thrombosis. However, conventional anticoagulants have serious side-effects, narrow therapeutic windows, and lack safe reversal agents (antidotes). Here, an alternative RNA origami displaying RNA aptamers as target-specific anticoagulant, is described. Improved design and construction techniques for self-folding, single-molecule RNA origami as a platform for displaying pre-selected RNA aptamers with precise orientational and spatial control, are reported. Nuclease resistance is added using 2’-fluoro-modified pyrimidines duringin vitrotranscription. When four aptamers are displayed on the RNA origami platform, the measured thrombin inhibition and anticoagulation activity is higher than observed for free aptamers, ssRNA-linked RNA aptamers, and RNA origami displaying fewer aptamers. Importantly, thrombin inhibition is immediately switched off by addition of specific reversal agents. Results for ssDNA and ssPNA (peptide nucleic acid) antidotes show restoration of 75% and 95% coagulation activity, respectively. To demonstrate potential for practical, long-term storage for clinical use, RNA origami was freeze-dried, and stored at room temperature. Freshly produced and freeze-dried RNA show identical levels of activity in coagulation assays. Compared to current commercial intravenous anticoagulants, RNA origami-based molecules show promise as safer alternatives with rapid activity switching for future therapeutic applications.
The genetic architecture of medication-use
Authors: Rohde Palle Duun , Sørensen Peter , Nyegaard Mette
Published: October 2020

Genomics has been forecasted to revolutionise human health by improving medical treatment through a better understanding of the molecular mechanisms of human diseases. Despite great successes of the last decade’s genome-wide association studies (GWAS), the results have to a limited extent been translated to genomic medicine. We propose, that one route to get closer to improved medical treatment is by understanding the genetics of medication-use. Here we obtained entire medication profiles from 335,744 individuals from the UK Biobank and performed a GWAS to identify which common genetic variants are major drivers of medication-use. We analysed 9 million imputed genetic variants, estimated SNP heritability, partitioned the genomic variance across functional categories, and constructed genetic scores for medication-use. In total, 59 independent loci were identified for medication-use and approximately 18% of the total variation was attributable to common genetic (minor allele frequency >0.01) variants. The largest fraction of variance was captured by variants with low to medium minor allele frequency. In particular coding and conserved regions, as well as transcription start sites, displayed significantly enrichment of heritability. The average correlation between medication-use and predicted genetic scores was 0.14. These results demonstrate that medication-useper seis a highly polygenic complex trait and that individuals with higher genetic liability are on average more diseased and have a higher risk for adverse drug reactions. These results provide an insight into the genetic architecture of medication use and pave the way for developments of multicomponent genetic risk models that includes the genetically informed medication-use.
Virtual brain grafting: Enabling whole brain parcellation in the presence of large lesions
Authors: Radwan Ahmed M. , Emsell Louise , Blommaert Jeroen , Zhylka Andrey , Kovacs Silvia , Theys Tom , Sollmann Nico , Dupont Patrick , Sunaert Stefan
Published: October 2020

Brain atlases and templates are at the heart of neuroimaging analyses, for which they facilitate multimodal registration, enable group comparisons and provide anatomical reference. However, as atlas-based approaches rely on correspondence mapping between images they perform poorly in the presence of structural pathology. Whilst several strategies exist to overcome this problem, their performance is often dependent on the type, size and homogeneity of any lesions present. We therefore propose a new solution, referred to as Virtual Brain Grafting (VBG), which is a fully-automated, open-source workflow to reliably parcellate MR images in the presence of a broad spectrum of focal brain pathologies, including large, bilateral, intra- and extra-axial, heterogeneous lesions with and without mass effect.

The core of the VBG approach is the generation of a lesion-free T1-weighted input image which enables further image processing operations that would otherwise fail. Here we validated our solution based on Freesurfer recon-all parcellation in a group of 10 patients with heterogeneous gliomatous lesions, and a realistic synthetic cohort of glioma patients (n=100) derived from healthy control data and patient data.

We demonstrate that VBG outperforms a non-VBG approach assessed qualitatively by expert neuroradiologists and Mann-Whitney U tests to compare corresponding parcellations (real patients U(6,6) = 33, z = 2.738, P < .010, synthetic patients U(48,48) = 2076, z = 7.336, P < .001). Results were also quantitatively evaluated by comparing mean dice scores from the synthetic patients using one-way ANOVA (unilateral VBG = 0.894, bilateral VBG = 0.903, and non-VBG = 0.617, P < .001). Additionally, we used linear regression to show the influence of lesion volume, lesion overlap with, and distance from the Freesurfer volumes of interest, on labelling accuracy.

VBG may benefit the neuroimaging community by enabling automated state-of-the-art MRI analyses in clinical populations, for example by providing input data for automated solutions for fiber tractography or resting-state fMRI analyses that could also be used in the clinic. To fully maximize its availability, VBG is provided as open software under a Mozilla 2.0 license (https://github.com/KUL-Radneuron/KUL_VBG).

Graphical abstract:

(A) shows T1 images from two patients with gliomatous lesions. VBG is a lesion replacement/filling workflow with one approach for unilateral lesions (uVBG) and another for bilateral lesions (bVBG). (B) shows the recon-all approach selected, (C) & (D) show the output, tissue segmentations (C) and whole brain parcellations (D). If VBG is not used (non-VBG) recon-all may finish with some errors in the parcellations (left) or fail to generate a parcellation entirely (right). However, using either VBG method allows recon-all to complete where it had previously failed and also improves parcellation quality.
Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment
Authors: Pauken Kristen E. , Shahid Osmaan , Lagattuta Kaitlyn A. , Mahuron Kelly M. , Luber Jacob M. , Lowe Margaret M. , Huang Linglin , Delaney Conor , Long Jaclyn M. , Fung Megan E. , Newcomer Kathleen , Tsai Katy K. , Chow Melissa , Guinn Samantha , Kuchroo Juhi R. , Burke Kelly P. , Schenkel Jason M. , Rosenblum Michael D. , Daud Adil I. , Sharpe Arlene H. , Singer Meromit
Published: October 2020

The ability to monitor anti-tumor CD8+T cell responses in the blood has tremendous therapeutic potential. Here, we used paired single-cell RNA sequencing and T cell receptor (TCR) sequencing to detect and characterize “tumor matching” (TM) CD8+T cells in the blood of mice with MC38 tumors and melanoma patients using the TCR as a molecular barcode. TM cells showed increased activation compared to non-matching T cells in blood, and appeared less exhausted than matching counterparts in tumor. Importantly, PD-1, which has been used to identify putative circulating anti-tumor CD8+T cells, showed poor sensitivity for identifying TM cells. By leveraging the transcriptome we identified candidate cell surface marker panels for TM cells in mice and melanoma patients, and validated NKG2D, CD39, and CX3CR1 in mice. These data demonstrate that the TCR can be used to identify tumor-relevant populations for comprehensive characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells.

Using single-cell RNA-sequencing coupled with TCR sequencing, we detected CD8+T cell clones shared between blood and tumor in mice and melanoma patients, characterized these matching clones in blood and tumor, and identified potential biomarkers for their isolation in blood.
Cryo-electron tomography of the herpesvirus procapsid reveals interactions of the portal with the scaffold and a shift on maturation
Authors: Buch Michael H. C. , Newcomb William W. , Winkler Dennis C. , Steven Alasdair C. , Heymann J. Bernard
Published: October 2020

Herpes simplex virus type 1 (HSV-1) requires seven proteins to package its genome through a vertex in its capsid, one of which is the portal protein, pUL6. The portal protein is also thought to facilitate assembly of the procapsid. While the portal has been visualized in mature capsids, we aimed to elucidate its role in the assembly and maturation of procapsids using cryo-electron tomography. We identified the portal vertex in individual procapsids, calculated a subtomogram average, and compared that with the portal vertex in empty mature capsids (A-capsids). The resulting maps show the portal on the interior surface with its narrower end facing outwards, while maintaining close contact with the capsid shell. In the procapsid, the portal is embedded in the underlying scaffold, suggesting that assembly involves a portal – scaffold complex. During maturation, the capsid shell angularizes with a corresponding outward movement of the vertices. We found that in A-capsids, the portal translocates further than the adjacent capsomers and strengthens its contacts with the capsid shell. Our methodology also allowed us to determine the number of portal vertices in each capsid, with most having one per capsid, but some none or two, and rarely three. The predominance of a single portal per capsid supports facilitation of the assembly of the procapsid.

Importance

Herpes simplex virus type 1 (HSV-1) infects a majority of humans, causing mostly mild disease but in some cases progressing towards life-threatening encephalitis. Understanding the life cycle of the virus is important to devise countermeasures. Production of the virion starts with the assembly of an icosahedral procapsid including DNA packaging proteins at a vertex, one of which is the dodecameric portal protein. The procapsid then undergoes maturation and DNA packaging through the portal, driven by a terminase complex. We used cryo-electron tomography to visualize the portal in procapsids and compare them to mature empty capsids. We found the portal located inside one vertex interacting with the scaffold protein in the procapsid. On maturation, the scaffold dissociates, the capsid angularizes, and the portal moves outward, associating closely with the capsid shell. These transformations may provide a basis for the development of drugs to prevent HSV-1 infections.
Detection of stress functional responses in bacterial populations under dry soil conditions show potential microbial mechanisms to resist drought conditions
Authors: Sarkar Soumyadev , Ward Kaitlyn , Jansson Janet K. , Lee Sonny T.M.
Published: October 2020

Climate change is predicted to have a negative effect on the grasslands of the United States and will be detrimental to the economy and environment. The changing precipitation levels would also have an effect on the structural and functional potential of associated soil microbiome communities, which in turn will regulate the health of the plants during stressful conditions. In this study, we applied metagenomics analyses to capture the responses of the bacterial populations under drier soil conditions. We collected soil from two sites (dry and wet) at the Konza Long-Term Ecological Research field station in Kansas, which had characteristic features of the native prairies. Soil drying resulted in a significant shift in the bacterial population at the community level. Following that, fifteen bacterial genomes were short-listed based on the availability in the public database, higher relative abundance in dry soils than in wet, and also according to their contributions in drier soil. The potential microbial mechanisms were elucidated when an in-depth analysis of the functional genes was performed. Translation elongation factor EF-Tu, thiamine biosynthesis protein, and catalase were identified as a part of the overall stress functional responses in the bacterial population in this study. We speculate that these identified bacterial populations are important for maintaining the health of the soil under dry conditions. Genes and/or pathways found in this study provide insights into microbial mechanisms that these bacterial populations might employ to resist challenging drought conditions.
SARS-CoV-2 viral budding and entry can be modeled using virus-like particles
Authors: Plescia Caroline B. , David Emily A. , Patra Dhabaleswar , Sengupta Ranjan , Amiar Souad , Su Yuan , Stahelin Robert V.
Published: October 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first discovered in December 2019 in Wuhan, China and expeditiously spread across the globe causing a global pandemic. While a select agent designation has not been made for SARS-CoV-2, closely related SARS-CoV-1 and MERS coronaviruses are classified as Risk Group 3 select agents, which restricts use of the live viruses to BSL-3 facilities. Such BSL-3 classification make SARS-CoV-2 research inaccessible to the majority of functioning research laboratories in the US; this becomes problematic when the collective scientific effort needs to be focused on such in the face of a pandemic. In this work, we assessed the four structural proteins from SARS-CoV-2 for their ability to form viruslike particles (VLPs) from human cells to form a competent system for BSL-2 studies of SARS-CoV-2. Herein, we provide methods and resources of producing, purifying, fluorescently and APEX2-labeling of SARS-CoV-2 VLPs for the evaluation of mechanisms of viral budding and entry as well as assessment of drug inhibitors under BSL-2 conditions.
Recruitment of Neuronal KCNQ2/3 Channels to Membrane Microdomains by Palmitoylation of Alzheimer’s Disease-Related Protein BACE1
Authors: Dai Gucan
Published: October 2020

β-secretase 1 (β-site amyloid precursor protein (APP)-cleaving enzyme 1, BACE1) plays a crucial role in the amyloidogenesis of Alzheimer’s Disease (AD). BACE1 was also discovered to act like an auxiliary subunit to modulate neuronal KCNQ2/3 channels independent of its proteolytic function. BACE1 is palmitoylated at its carboxyl-terminal region, which brings BACE1 to ordered, cholesterol-rich membrane microdomains (lipid rafts). However, the physiological consequences of this specific localization of BACE1 remain elusive. Using spectral Förster Resonance Energy Transfer (FRET), BACE1 and KCNQ2/3 channels were confirmed to form a signaling complex, a phenomenon that was relatively independent of the palmitoylation of BACE1. Nevertheless, palmitoylation of BACE1 was required for recruitment of KCNQ2/3 channels to lipid-raft domains. Two fluorescent probes designated L10 and S15, were used to label lipid-raft and non-raft domains of the plasma membrane, respectively. Coexpressing BACE1 substantially elevated the FRET between L10 and KCNQ2/3 whereas the BACE1-4C/A quadruple mutation failed to produce this effect. In contrast, BACE1 had no significant effect on the FRET between S15 probes and KCNQ2/3 channels. A reduction of BACE1-dependent FRET between raft-targeting L10 probes and KCNQ2/3 channels by applying cholesterol-extracting reagent methyl-β-cyclodextrin (MβCD), raft-disrupting general anesthetics, or pharmacological inhibitors of palmitoylation all supported our hypothesis of the palmitoylation-dependent and raft-specific localization of KCNQ2/3 channels. Furthermore, mutating the four carboxyl-terminal cysteines (4C/A) of BACE1 abolished the BACE1-dependent increase of FRET between KCNQ2/3 and a lipid raft-specific protein caveolin 1. Collectively, we propose how the AD-related protein BACE1 underlies the localization of a neuronal potassium channel.
Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6
Authors: Selmi Tommaso , Hussain Shobbir , Dietmann Sabine , Heiss Matthias , Carter Jean-Michel , Dennison Rebecca , Flad Sophia , Huang Ya-Lin , Kellner Stefanie , Bornelöv Susanne , Frye Michaela
Published: October 2020

Methylation is the most common internal modification in mRNA. While the highly abundant N6-methyladonsine (m6A) modification affects most aspects of mRNA function, the precise functions of the rarer 5-methylcytosine (m5C) remains largely unknown. Here, we map m5C in the human transcriptome using methylation-dependent individual-nucleotide resolution cross-linking and immunoprecipitation (miCLIP) combined with RNA bisulfite sequencing. We identify NSUN6 as a methyltransferase with strong substrate specificity towards mRNA. NSUN6 primarily targeted three prime untranslated regions (3’UTR) at the consensus sequence motif CTCCA, located in loops of hairpin structures. Knockout and rescue experiments revealed that only mRNA methylation sites containing the consensus motif depended on the presence of NSUN6. Furthermore, ribosome profiling demonstrated that NSUN6-specific consensus motifs marked translation termination. However, even though NSUN6-methylated mRNAs were reduced in NSUN6 knockout cells, NSUN6 was dispensable for mouse embryonic development. Thus, our study identifies NSUN6 as methyltransferase targeting mRNA in a sequence- and structure-specific manner.
The cerebellar clock: predicting and timing somatosensory touch
Authors: Andersen Lau M. , Dalal Sarang S.
Published: October 2020

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The prediction of sensory feedback is known to involve the cerebellum, but its precise nature and timing have remained unclear due to the scarcity of time-sensitive cerebellar neuroimaging studies. We here, using magnetoencephalography in human participants, investigated the working hypothesis that one function of the cerebellum is to predict exactly when rhythmic stimuli are expected to impinge on sensory receptors.

We compared the cerebellum’s response between somatosensory omissions embedded in perfectly rhythmic versus jittered trains of stimulation. At the precise moment that an omitted stimulus would have appeared, the cerebellum exhibited a beta band (14-30 Hz) response that was stronger when preceded by a perfectly rhythmic sequence. Meanwhile, the rhythm of new stimulation sequences induced theta band (4-7 Hz) activity in the cerebellum.

Our results provide evidence that the cerebellum acts as a clock that entrains to rhythmic stimuli, likely for the purpose of detecting any deviations from that rhythm.