bluuebunny/crossref_metadata_2025 huggingface dataset:
Essential amino acid formulations to prevent mitochondrial dysfunction and oxidative stress
Authors: Ruocco Chiara , Segala Agnese , Valerio Alessandra , Nisoli Enzo
Published: October 2020

Purpose of review

Both restriction and supplementation of specific amino acids or branched-chain amino acids (BCAAs) are described to improve metabolic homeostasis, energy balance, and health span. This review will discuss the recent findings of the role of amino acid supplements in the regulation of mitochondrial health.

Recent findings

A mixture of essential amino acids (EAAs), BCAA enriched mixture, was found to extend healthy life span in elderly mice and prevent multiple diseases associated with an energy deficit, similarly to caloric restriction or fasting-mimicking diets. A growing body of evidence highlights mitochondria as the central target of this supplement: it promotes mitochondrial biogenesis and the activation of antioxidant defence systems in different physiological (e.g., exercise or ageing) or pathological conditions (e.g., sarcopenia, muscular dystrophy, liver steatosis, or impaired cognition). Based on these results, new formulas have been created enriched with Krebs cycle substrates, behaving more efficiently than BCAA enriched mixture.

EAA-BCAA balanced supplements might be valuable not only for healthy individuals undergoing to energy deficit (e.g., athletes) during strenuous exercise or training but also against diseases characterized by a dysregulated catabolic state or mitochondrial dysfunction, such as age-related disorders. The associated mechanistic processes should be identified as potential pharmacological targets.
Inherited disorders of sulfur amino acid metabolism: recent advances in therapy
Authors: Kožich Viktor , Majtan Tomas
Published: October 2020

Purpose of review

Metabolism of sulfur amino acids (SAA) provides compounds important for many cellular functions. Inherited disorders of SAA metabolism are typically severe multisystemic diseases affecting brain, liver, connective tissue, or vasculature. The review summarizes the present therapeutic approaches and advances in identifying novel treatment targets, and provides an overview of new therapies.

Recent findings

Current treatments of genetic disorders of SAA metabolism are primarily based on modulation of affected pathways by dietary measures and provision of lacking products or scavenging of toxic molecules. Recent studies identified additional therapeutic targets distant from the primary defects and explored ideas envisioning novel treatments, such as chaperone and gene therapy. Recombinant protein production and engineering resulted in development and clinical testing of enzyme therapies for cystathionine β-synthase deficiency, the most common inborn error of SAA metabolism.

Complex regulation of pathways involved in SAA metabolism and cellular consequences of genetic defects in SAA metabolism are only partially understood. There is a pressing need to increase substantially our knowledge of the disease mechanisms to develop more effective therapies for patients suffering from these rare disorders.
Protein and amino acids in nonalcoholic fatty liver disease
Authors: Tricò Domenico , Biancalana Edoardo , Solini Anna
Published: October 2020

Purpose of review

In this review, the latest evidence on the influence of dietary protein and plasma amino acids in the pathogenesis of nonalcoholic fatty liver disease (NAFLD) is discussed.

Recent findings

Increasing protein consumption during weight loss and maintenance may help reduce liver fat content. Conversely, high protein intake characteristic of the unhealthy Western diet is associated with increased NAFLD prevalence and severity. Plasma concentration of several amino acids, including branched-chain (BCAA) and aromatic amino acids (AAA), is altered in NAFLD. Excess amino acid availability contributes to intrahepatic fat accumulation and may reflect poor dietary habits and dysregulation of amino acid metabolic processing in both liver and peripheral tissues. Specific amino acid patterns, characterized by increased BCAA, AAA, alanine, glutamate, lysine levels, and decreased glycine and serine levels, may be used for early detection of NAFLD and noninvasive assessment of its histological severity.

Mechanistic studies in NAFLD have been mostly focused on carbohydrate and fat metabolism, while little is known about the influence of protein and amino acids. Moreover, intervention and observational studies on the relation between protein intake and NAFLD yielded conflicting results. Filling the current knowledge gaps would help define the optimal diet composition for NAFLD prevention and management. Furthermore, metabolomics studies may provide insight into the pathogenesis of NAFLD, identify useful diagnostic and prognostic biomarkers, and unravel novel pharmacological targets and treatment options.
Pepsin in gastroesophageal and extraesophageal reflux: molecular pathophysiology and diagnostic utility
Authors: Samuels Tina L. , Johnston Nikki
Published: October 2020

Purpose of review

Gastroesophageal and extraesophageal reflux are prevalent and costly diseases. Recognition of the pathogenicity of nonacid reflux has stimulated interest in alternatives to acid-targeting diagnostics and therapeutics. Pepsin is the most deleterious enzyme in refluxate, eliciting inflammatory and carcinogenic effects irrespective of acid. Its presence in all refluxate and detection in saliva have situated pepsin as the most widely researched biomarker for reflux today. This review summarizes emerging findings regarding pepsin-mediated damage during reflux and developments in pepsin-targeting diagnostics.

Recent findings

New evidence supports a role for pepsin in epithelial--mesenchymal transition, an important process in carcinogenesis and fibrosis. The first global transcriptomic analysis of pepsin-exposed laryngeal cells was described, yielding evidence of a putative airway pepsin receptor. Evaluation of pepsin diagnostics highlighted the need for rigorous validation in which pepsin concentrations are corroborated by a secondary quantitative assay, and reflux is confirmed or excluded by multichannel intraluminal impedance pH testing. Standards for sample collection and storage, and normative and pathological values are lacking.

Progress continues to be made in our understanding of pepsin-mediated damage with implications for novel therapeutic strategies. Salivary pepsin diagnostics continue to garner interest; however, further work appears necessary to improve their accuracy and reproducibility.
Trauma patients in the pediatric ICU: rational use of a limited resource
Authors: Arshad Ahmed , Polcari Ann M. , Pinto Neethi P. , Slidell Mark B.
Published: October 2020

Purpose of review

Traumatic injuries are a leading cause of pediatric mortality; pediatric ICUs (PICUs) are an important but potentially limited resource associated with high costs. In an era of rising healthcare costs, appropriate resource utilization is important. Here, we examine evidence-based guidelines supporting the management of pediatric traumatic injury outside of the PICU.

Recent findings

Historical management of solid organ injury and traumatic brain injury was focused on operative management. However, over the past four decades, management of solid organ injury has shifted from invasive management to nonsurgical management with a growing body of evidence supporting the safety and efficacy of this trend. The management of traumatic brain injury (TBI) has had a similar evolution to that of solid organ injury with regard to nonoperative management and management outside the critical care setting.

The use of evidence-based guidelines to support expectant management in the setting of pediatric trauma has the potential to reduce unnecessary resource utilization of the PICU. In this review, we present findings that support nonoperative management and management of pediatric trauma outside of the PICU setting. In resource-poor areas, this approach may facilitate care for pediatric trauma patients. The implications are also important in resource-rich settings because of the unintended risks associated with PICU.
Two Cases With Features of Lymphocyte Variant Hypereosinophilic Syndrome With STAT3 SH2 Domain Mutations
Authors: Fernandez-Pol Sebastian , Petersen Bruce , Murphy Jo-Ellen , Oak Jean S. , Wang Erica B.K. , Rieger Kerri E. , Kim Youn H. , Khodadoust Michael S. , Suarez Carlos J.
Published: October 2020

Lymphocyte variant hypereosinophilic syndrome (LV-HES) is a rare cause of eosinophilia that is due to eosinophilipoietic cytokine production by an immunophenotypically abnormal T-cell clone. The molecular pathogenesis of this disorder is largely unknown and only 1 case of LV-HES with a pathogenic STAT3 mutation has been described thus far. Here we report 2 cases of LV-HES with STAT3 SH2 domain mutations. These cases further support the model that activation of STAT3 signaling through STAT3 SH2 domain mutations is a recurrent event in LV-HES.
Improving the Safety of an Emergency Department-Based Direct Admission Process at a Children's Hospital
Authors: Huy Tess , Lowrie Lia , Flood Robert , Chambers Rebecca , Weiss Nancy , Nordike Keith , Wathen David
Published: October 2020

Objectives

Direct admission refers to admitting a patient to a unit avoiding usual entry points such as the emergency department. Inappropriate placement of direct admissions can result in rapid response activations, codes and unanticipated pediatric intensive care unit (PICU) transfers, which correlate with higher mortality and longer lengths of stay. The objective of the project was to improve the safety of the direct admission process as evidenced by decreasing the transfer of direct admission patients to the PICU within 6 hours.

Methods

Utilizing the model for improvement, a multidisciplinary team was assembled to improve our screening process and reduce unanticipated direct admission-to-PICU transfers within 6 hours of arrival. Our emergency department–based direct admission process includes screening vital signs (temperature, heart rate, respiratory rate, blood pressure, and pulse oximetry) and a Pediatric Early Warning Score. Five Plan-Do-Study-Act cycles focused on role definition, improved documentation, referring facility and family awareness, improved visual management within the ED, and education of partner EMS and transport providers. The primary outcome was PICU transfer within 6 hours of direct admission arrival. Compliance with full screening was a process measure and number of direct admissions a balancing measure. Statistical process control charts and run charts were used to follow the measures.

Results

The total number of direct admissions from January 2014 to the end of data collection, June 2018, was 3070 patients. Screening protocol compliance improved from 56% to over 80% for the entire hospital. Unanticipated direct admission-to-PICU transfers decreased from a baseline of 1 every 98 patients to a special cause of 1 in 1126 patients.

Conclusions

By utilizing QI methodology our team was able to implement and sustain a direct admission process that was more consistent, easier to document and improved the safety of our patients. Our study demonstrates that screening direct admissions reliably and consistently can decrease the rate of unanticipated transfer to a higher level of care.
Antiplatelet and anticoagulant agents have minimal impact on traumatic brain injury incidence, surgery, and mortality in geriatric ground level falls: A multi-institutional analysis of 33,710 patients
Authors: Fakhry Samir M. , Morse Jennifer L. , Garland Jeneva M. , Wilson Nina Y. , Shen Yan , Wyse Ransom J. , Watts Dorraine D.
Published: October 2020

BACKGROUND

Falls are the leading cause of traumatic brain injury (TBI) and TBI-related deaths for older persons (age, ≥65 years). Antiplatelet and/or anticoagulant therapy (antithrombotics [ATs]) is generally felt to increase this risk, but the literature is inconsistent. The purpose of this study was to determine the impact of AT use on the rate, severity, and outcomes of TBI in older patients following ground level falls.

METHODS

Ground level fall patients from 90 hospitals’ trauma registries were selected. Patients were excluded if younger than 65 years or had an Abbreviated Injury Scale score of >2 in a region other than head. Electronic medical record data for preinjury AT therapy were obtained. Patients were grouped by regimen for no AT, single, or multiple agents. Groups were compared on rates of diagnosed TBI, TBI surgery, and mortality.

RESULTS

There were 33,710 patients (35% male; mean age, 80.5 years; mean Glasgow Coma Scale, 14.6), with 47.6% on single or combination AT therapy. The proportion of patients with TBI diagnoses did not differ between those on no AT (21.25%) versus AT (21.61%; p = 0.418). Apixaban (15.7%; p < 0.001) and rivaroxaban (13.19%; p = 0.011) were associated with lower rates of TBI, and acetylsalicylic acid-clopidogrel was associated with a higher TBI rate (24.34%; p = 0.002) versus no AT. acetylsalicylic acid-clopidogrel was associated with a higher cranial surgery rate (2.9%; p = 0.006) versus no AT (1.96%), but surgery rates were similar for all other regimens. No regimen was associated with higher mortality.

CONCLUSION

In this large multicenter study, the intake of ATs in older patients with ground level falls was associated with inconsistent effects on risk of TBI and no significant increases in mortality, indicating that AT use may have negligible impact on patient clinical management. A large, confirmatory, prospective study is needed because the commonly held belief that ATs uniformly increase the risk of traumatic intracranial bleeding and mortality is not supported.

LEVEL OF EVIDENCE

Therapeutic/care management, level II.
Structural stability of SARS-CoV-2 degrades with temperature
Authors: Sharma A. , Preece B. , Swann H , Fan X. , McKenney R.J. , Ori-McKenney K.M. , Saffarian S. , Vershinin M.D.
Published: October 2020

SARS-CoV-2 is a novel coronavirus which has caused the COVID-19 pandemic. Other known coronaviruses show a strong pattern of seasonality, with the infection cases in humans being more prominent in winter. Although several plausible origins of such seasonal variability have been proposed, its mechanism is unclear. SARS-CoV-2 is transmitted via airborne droplets ejected from the upper respiratory tract of the infected individuals. It has been reported that SARS-CoV-2 can remain infectious for hours on surfaces. As such, the stability of viral particles both in liquid droplets as well as dried on surfaces is essential for infectivity. Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. We demonstrate that even a mild temperature increase, commensurate with what is common for summer warming, leads to dramatic disruption of viral structural stability, especially when the heat is applied in the dry state. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter.

Statement of Scientific Significance

The economic and public health impact of the COVID-19 pandemic are very significant. However scientific information needed to underpin policy decisions are limited partly due to novelty of the SARS-CoV-2 pathogen. There is therefore an urgent need for mechanistic studies of both COVID-19 disease and the SARS-CoV-2 virus. We show that individual virus particles suffer structural destabilization at relatively mild but elevated temperatures. Our nanoscale results are consistent with recent observations at larger scales. Our work strengthens the case for COVID-19 resurgence in winter.
Circulating tumour cell and cell-free DNA kinetics during radiotherapy in patients with intact head and neck squamous cell carcinoma
Authors: Ng Sweet Ping , Hall Carolyn S , Meas Salyna , Sarli Vanessa N , Bahig Houda , Cardenas Carlos E , Elgohari Baher , Wang JiHong , Johnson Jason M , Moreno Amy C , Skinner Heath , Garden Adam S , Na Lumine , Yuan Ying , Urbauer Diana , Phan Jack , Gunn G Brandon , Frank Steven J , Shah Shalin , Rosenthal David I , Morrison William H , MacManus Michael P , Fuller Clifton D , Lucci Anthony
Published: October 2020

Head and neck squamous cell carcinoma (HNSCC) treatment response relies heavily on macroscopic clinical findings. Blood monitoring of circulating markers during treatment may improve earlier detection of responders versus non-responders during radiotherapy. In this study, patients with intact tumour of HNSCC were enrolled in the prospective PREDICT-HN study. Pre-, after first treatment, weekly, and post-treatment blood samples were collected. CTC was enumerated using the CellSearch system. cfDNA was quantified from cfNA isolated at pre-, mid- and post-treatment timepoints. Blood samples were collected from 45 patients. Of the 339 samples analysed for CTC, 31% had detectable CTCs. Nine patients had detectable CTCs (1-3/7.5ml blood) in pre-treatment samples. After 1 fraction, 16 patients had CTCs detected, with 12 who had no pre-treatment CTC. Sixteen (36%) patients had detectable CTC in final week of treatment. There was no correlation between cancer stage, nodal status and tumour burden with CTC. cfDNA levels increased during treatment, with its highest level in the final week and lowest at post-treatment. Our results showed in HNSCC that CTCs can be detected during radiotherapy, suggesting mobilization into circulation during treatment, with as-yet-unknown viability. cfDNA kinetics during treatment correlated with CTC release, and may indicate apoptotic change.

Simple Summary

Head and neck squamous cell carcinoma (HNSCC) treatment response relies heavily on macroscopic clinical findings. Blood monitoring of circulating markers such as circulating tumour cell (CTC) and cell-free DNA (cfDNA) during treatment may improve earlier detection of responders versus non-responders during definitive radiotherapy. Although the detection of CTCs and cfDNA in patients with HNSCC has been described, there is minimal data on the kinetics of CTC counts and cfDNA levels during radiotherapy in patients with HNSCC. Here, our study prospectively describes the changes in CTC and cfDNA enumeration during radiotherapy in patients with HNSCC. Our results showed, for the first time to our knowledge, in HNSCC, that CTCs can be detected during radiotherapy, suggesting mobilization into peripheral circulation during treatment, with as-yet-unknown viability. cfDNA kinetics during treatment correlated with CTC release, may indicate apoptotic change during radiotherapy. Combined cfDNA-CTC as an early marker of treatment response should be investigated further.
Development of a deep learning classifier to accurately distinguish COVID-19 from look-a-like pathology on lung ultrasound
Authors: Arntfield Robert , VanBerlo Blake , Alaifan Thamer , Phelps Nathan , White Matt , Chaudhary Rushil , Ho Jordan , Wu Derek
Published: October 2020

Objectives

Lung ultrasound (LUS) is a portable, low cost respiratory imaging tool but is challenged by user dependence and lack of diagnostic specificity. It is unknown whether the advantages of LUS implementation could be paired with deep learning techniques to match or exceed human-level, diagnostic specificity among similar appearing, pathological LUS images.

Design

A convolutional neural network was trained on LUS images with B lines of different etiologies. CNN diagnostic performance, as validated using a 10% data holdback set was compared to surveyed LUS-competent physicians.

Setting

Two tertiary Canadian hospitals.

Participants

600 LUS videos (121,381 frames) of B lines from 243 distinct patients with either 1) COVID-19, Non-COVID acute respiratory distress syndrome (NCOVID) and 3) Hydrostatic pulmonary edema (HPE).

Results

The trained CNN performance on the independent dataset showed an ability to discriminate between COVID (AUC 1.0), NCOVID (AUC 0.934) and HPE (AUC 1.0) pathologies. This was significantly better than physician ability (AUCs of 0.697, 0.704, 0.967 for the COVID, NCOVID and HPE classes, respectively), p < 0.01.

Conclusions

A deep learning model can distinguish similar appearing LUS pathology, including COVID-19, that cannot be distinguished by humans. The performance gap between humans and the model suggests that subvisible biomarkers within ultrasound images could exist and multi-center research is merited.
Longitudinal survey reveals delayed effects of forager gene expression on stingless bee colony health
Authors: Caesar Lílian , Lopes Anelise Martins Correa , Radaeski Jefferson Nunes , Bauermann Soraia Girardi , Konzen Enéas Ricardo , Pombert Jean-François , Sattler Aroni , Blochtein Betina , Carvalho Airton Torres , Haag Karen Luisa
Published: October 2020

Bee populations are declining globally due to different environmental stressors, such as pathogens, malnutrition, and agrochemicals. Brazil is the home of hundreds of stingless bee species, some of them now considered endangered, though very little is known about the impact of disease on native bees. In Southern Brazil the endangered stingless beeMelipona quadrifasciatais affected by an annual syndrome that causes sudden death of workers, eventually leading colonies to collapse. Although novel viruses were found in foragers from diseased colonies, none has been consistently implicated in the outbreak. Here we used transcriptomics in combination with an integrative longitudinal survey on managed colonies to identify predictors for preventingM. quadrifasciatacolony failures. We found that key genes related to xenobiotic metabolization, nutrition and immune responses are downregulated in foragers from colonies that became diseased three months later. The period that preceded the outbreak was marked by pronounced forager weight loss as well as behavioural changes. Our findings support the proposition that worldwide bee mortality is influenced by a combination of diverse sublethal factors, and increase awareness of the long-term effects of genetic diversity erosion in stingless bee species, which enhances their vulnerability to environmental stressors.
DNA Methyltransferase Inhibitors with Novel Chemical Scaffolds
Authors: Juárez-Mercado K. Eurídice , Prieto-Martínez Fernando D. , Sánchez-Cruz Norberto , Peña-Castillo Andrea , Prada-Gracia Diego , Medina-Franco José L.
Published: October 2020

Inhibitors of DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug discovery. They are also chemical tools to understand the biochemistry of epigenetic processes. Herein, we report five distinct inhibitors of DNMT1 characterized in enzymatic inhibition assays that did not show activity with DNMT3B. It was concluded that the dietary component theaflavin is an inhibitor of DNMT1. Two additional novel inhibitors of DNMT1 are the approved drugs glyburide and panobinostat. The DNMT1 enzymatic inhibitory activity of panobinostat, a known pan inhibitor of histone deacetylases, agrees with experimental reports of its ability to reduce DNMT1 activity in liver cancer cell lines. Molecular docking of the active compounds with DNMT1, and re-scoring with the recently developed Extended Connectivity Interaction Features approach, had an excellent agreement between the experimental IC50values and docking scores.
High-resolution architecture of human epiphysis formation
Authors: Sun Heng , Wen Ya , Wu Weiliang , Qin Tian , An Chengrui , Fan Chunmei , Chen Yishan , Ji Junfeng , Chew Ting Gang , Chen Jiansong , Ouyang Hongwei
Published: October 2020

Human limb skeletal system consists of both bone and cartilage which originated from fetal cartilage. However, the roadmap of chondrocyte divergent differentiation to bone and articular cartilage has yet to be established. Epiphysis possesses articular cartilage, growth plate and the secondary ossification center (SOC), making it an ideal model to uncover the trajectory of chondrocyte divergent differentiation. Here, we mapped differentiation trajectory of human chondrocyte during postnatal finger epiphysis development by using single-cell RNA sequencing. Our results uncovered that chondroprogenitors have two differentiation pathways to hypertrophic chondrocytes during ossification, and one pathway to articular chondrocytes for formation of cartilages. Interestingly, we found that, as an addition to the known typical endochondral ossification path from resting, proliferative to hypertrophic chondrocytes, there was a bypass by which chondroprogenitors differentiate into hypertrophic chondrocytes without proliferative stage. Furthermore, our results revealed two new chondrocyte subpopulations (bypass chondrocytes as it appeared in the ossification bypass, andID1+chondroblasts in articular chondrocyte path) during postnatal epiphysis development in addition to six well-known subpopulations. Overall, our study provides a comprehensive roadmap of chondrocyte differentiation in human epiphysis thereby expanding the knowledge of bone and articular cartilage, which could be utilized to design biotherapeutics for bone and articular cartilage regeneration.
The ubiquitylome of developing cortical neurons
Authors: Menon Shalini , Goldfarb Dennis , Cousins Emily M. , Major M. Ben , Gupton Stephanie L.
Published: October 2020

TRIM9 and TRIM67 are neuronally-enriched E3 ubiquitin. Both genes are required for neuronal morphological responses to the axon guidance cue netrin-1. For example, our previously published work demonstrated that the actin polymerase VASP and the netrin receptor DCC exhibit TRIM9 dependent ubiquitylation that is lost upon netrin stimulation. Deletion of either gene in the mouse results in subtle neuroanatomical anomalies yet overt deficits in spatial learning and memory. Despite their role in neuronal form and function, the identity of few TRIM9 or TRIM67 substrates are known. Here we performed ubiquitin remnant profiling approach in cultured wildtype and knockout murine embryonic cortical neurons to identify ubiquitylated peptides and proteins, with the ultimate goal of identifying substrates of TRIM9 and TRIM67 that exhibited reduced ubiquitylation in the absence of the ligase. This work reveals the ubiquitylome of developing cortical neurons.
Higher temperatures worsen the effects of mutations on protein stability
Authors: Kontopoulos Dimitrios - Georgios , Patmanidis Ilias , Barraclough Timothy G. , Pawar Samraat
Published: October 2020

Understanding whether and how temperature increases alter the effects of mutations on protein stability is crucial for understanding the limits to thermal adaptation by organisms. Currently, it is generally assumed that the stability effects of mutations are independent of temperature. Yet, mutations should become increasingly destabilizing as temperature rises due to the increase in the energy of atoms. Here, by performing an extensive computational analysis on the essential enzyme adenylate kinase in prokaryotes, we show, for the first time, that mutations become more destabilizing with temperature both across and within species. Consistent with these findings, we find that substitution rates of prokaryotes decrease nonlinearly with temperature. Our results suggest that life on Earth likely originated in a moderately thermophilic and thermally fluctuating environment, and indicate that global warming should decrease the per-generation rate of molecular evolution of prokaryotes.
Connecting high-resolution 3D chromatin organization with epigenomics
Authors: Feng Fan , Yao Yuan , Wang Xue Qing David , Zhang Xiaotian , Liu Jie
Published: October 2020

The resolution of chromatin conformation capture technologies keeps increasing, and the recent nucleosome resolution chromatin contact maps allow us to explore how fine-scale 3D chromatin organization is related to epigenomic states in human cells. Using publicly available Micro-C datasets, we have developed a deep learning model, CAESAR, to learn a mapping function from epigenomic features to 3D chromatin organization. The model accurately predicts fine-scale structures, such as short-range chromatin loops and stripes, that Hi-C fails to detect. With existing epigenomic datasets from ENCODE and Roadmap Epigenomics Project, we successfully imputed high-resolution 3D chromatin contact maps for 91 human tissues and cell lines. In the imputed high-resolution contact maps, we identified the spatial interactions between genes and their experimentally validated regulatory elements, demonstrating CAESAR’s potential in coupling transcriptional regulation with 3D chromatin organization at high resolution.
The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping
Authors: Wang Hai-Long
Published: October 2020

I performed whole-genome sequencing on SARS-CoV-2 collected from COVID-19 samples at Mayo Clinic Rochester in mid-April, 2020, generated 85 consensus genome sequences and compared them to other genome sequences collected worldwide. I proposed a novel illustrating method using a 2D map to display populations of co-occurring nucleotide variants for intra- and inter-viral clades. This method is highly advantageous for the new era of “big-data” when high-throughput sequencing is becoming readily available. Using this method, I revealed the emergence of inter-clade hybrid SARS-CoV-2 lineages that are potentially caused by homologous genetic recombination.
Digital imaging outperforms traditional scoring methods of spittlebug tolerance inUrochloa humidicolahybrids
Authors: Hernandez Luis M. , Espitia Paula , Castiblanco Valheria , Cardoso Juan A
Published: October 2020

American spittlebug complex (Hemiptera: Cercopidae) is a critical pest for existingUrochloa humidicolacultivars in the neotropical savannas. TheU. humidicolabreeding program of the International Center for Tropical Agriculture aims to increase tolerance to spittlebugs. To developU. humidicolagenotypes with superior tolerance to spittlebugs than existing cultivars, adequate screening methods ought to be deployed. Currently, visual scores of plant damage by spittlebugs is the standard method to screen for variation in plant tolerance. However, visual scoring is prone to human bias, is of medium throughput and relies of the expertise of well-trained personnel. In this study, we compared estimations of plant damage from two alternative methods (SPAD measurements and digital images) and visual scoring from an inexpert evaluator with the plant damage estimated from an expert. This information should instruct if different methods could be implemented in theU. humidicolabreeding program. Time needed to evaluate damage was recorded for each method. Lin’s correlation coefficient, Pearson’s correlation coefficient and broad sense heritability values were also calculated. Overall, damage estimated from digital images showed the highest throughput (twice as fast as visual scoring from an expert); high correlations with visual scoring (r> 0.80, p < 0.0001); and heritability values for plant damage as good or better (> 0.7) than those obtained by visual scoring from an expert. Our results indicate that digital imaging is a phenotyping method that might improve the efficiency of breeding for increased tolerance to spittlebugs inU. humidicola.

Highlight

Digital imaging outperformed standard scoring method of spittlebug tolerance inUrochloa humidicola,suggesting that this method might improve the efficiency of breeding for such stress.
TMTPro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level
Authors: Johnson Alex , Stadlmeier Michael , Wühr Martin
Published: October 2020

Multiplexed proteomics is a powerful tool to assay cell states in health and disease, but accurate quantification of relative protein changes is impaired by interference from co-isolated peptides. Interference can be reduced by using MS3-based quantification, but this reduces sensitivity and requires specialized instrumentation. An alternative approach is quantification by complementary ions, which allows accurate and precise multiplexed quantification at the MS2 level and is compatible with the most widely distributed instruments. However, complementary ions of the popular TMT tag form inefficiently and multiplexing is limited to five channels. Here, we evaluate and optimize complementary ion quantification for the recently released TMTPro tag, which increases plexing capacity to eight channels (TMTProC). We find that the beneficial fragmentation properties of TMTPro increase quantification signal five-fold compared to TMT. This increased sensitivity results in ~65% more proteins quantified compared to TMTPro-MS3 and even slightly outperforms TMTPro-MS2. Furthermore, TMTProC quantification is more accurate than TMTPro-MS2 and even superior to TMTPro-MS3. To demonstrate the power of TMTProC, we analyzed a human and yeast interference sample and were able to quantify 13,290 proteins in 24 fractions. Thus, TMTProC advances multiplexed proteomics data quality and widens access to accurate multiplexed proteomics beyond laboratories with MS3-capable instrumentation.
An absence of temporal filling-in at the physiological blind-spot
Authors: Dhupia Neha , Schwarzkopf D. Samuel , Arnold Derek H.
Published: October 2020

Visual objects that extend across physiological blind spots seem to encapsulate the extent of blindness, due to a process commonly referred to as a perceptual filling-in of spatial vision. It is unclear if temporal perception is similar, so we examined temporal relationships governing causality perception across the blind spot. We found the human brain does not allow for the time an object should take to traverse the blind-spot when engaging in a causal interaction. We also used electroencephalogram (EEG), to examine temporal signatures of elements flickering on and off in tandem, or in counter-phase. At a control site, we found more brain activity was entrained at the duty cycle by flicker relative to counter-phase changes, whereas these conditions were indistinguishable about blind spots. Our data suggest a common pool of neurons might encode temporal properties on either side of physiological blind-spots. This would explain the absence of any allowance for the extent of blindness in causality perception, and the weakened differences between temporal representations of flicker and counter-phased changes about the blind spot. Overall, our data suggest that, unlike spatial vision, there is no temporal filling-in for perceptual representations about physiological blind spots.
Assessing cerebellar-cortical connectivity using concurrent TMS-EEG: A Feasibility Study
Authors: Fernandez Lara , Biabani Mana , Do Michael , Opie George M. , Hill Aron T. , Barham Michael P. , Teo Wei-Peng , Byrne Linda K. , Rogasch Nigel C. , Enticott Peter G.
Published: October 2020

Background

Combined single-pulse transcranial magnetic stimulation (TMS) and electroencephalography (EEG) has been used to probe the features of local networks in the cerebral cortex. Here we investigate whether we can use this approach to explore long-range connections between the cerebellum and cerebral cortex.

Objective

To assess the feasibility of using cerebellar TMS-EEG for the exploration of cerebellar-cerebral network dynamics.

Methods

Ten healthy adults received single-pulse suprathreshold TMS to the cerebellum and an occipital/parietal control site with double-cone and figure-of-eight coils while cerebral activity was recorded. A multisensory electrical control condition was used to simulate the sensation of the double-cone coil at the cerebellar site. Two cleaning pipelines were compared, and the spatiotemporal relationships of the EEG output between conditions were examined at sensor and source levels.

Results

Cerebellar stimulation with the double-cone coil resulted in large artefacts in the EEG trace. The addition of SOUND filtering to the cleaning pipeline improved the signal such that further analyses could be undertaken. The cortical potentials evoked by the active TMS conditions showed strong relationships with the responses to the multisensory control condition after ~50 ms. A distinct parietal component at ~42 ms was found following cerebellar double-cone stimulation.

Conclusions

Cerebellar double-cone stimulation produces large artefacts in the EEG. Cerebellar-specific responses could not be reliably differentiated from sensory evoked potentials after ~50 ms. While evoked potentials differed across conditions at early latencies, it is unclear as to whether these represented TMS-related network activation of the cerebellarthalamocortical tract, or whether components were dominated by sensory contamination and/or coil-driven artefacts. Further work will be required to clarify the specific contribution of cerebellar-cortical connectivity to the observed early latency signals.
Effects ofNT5C2germline variants on 6-mecaptopurine metabolism in children with acute lymphoblastic leukemia
Authors: Jiang Chuang , Yang Wenjian , Moriyama Takaya , Liu Chengcheng , Smith Colton , Yang Wentao , Qian Maoxiang , Li Ziping , Tulstrup Morten , Schmieglow Kjeld , Crews Kristine R. , Zhang Hui , Pui Ching-Hon , Evans William , Relling Mary , Bhatia Smita , Yang Jun J.
Published: October 2020

6-mercaptopurine (6-MP) is widely used in the treatment of acute lymphoblastic leukemia (ALL), and its cytotoxicity is primarily mediated by thioguanine nucleotide metabolites (TGN). Recent genome-wide association study has identified germline polymorphisms (e.g., rs72846714) in theNT5C2gene associated with 6-MP metabolism in patients with ALL. However, the full spectrum of genetic variation inNT5C2is unclear and its impact on 6-MP drug activation has not been comprehensively examined. To this end, we performed targeted sequencing ofNT5C2in 588 children with ALL and identified 121 single nucleotide polymorphisms (SNPs) nominally associated with erythrocyte TGN during 6-MP treatment (P< 0.05). Of these, 61 variants were validated in a replication cohort of 372 children with ALL. After considering linkage disequilibrium and multivariate analysis, we confirmed two clusters of variants, represented by rs72846714 and rs58700372, that independently affected 6-MP metabolism. Functional studies showed that rs58700372 directly altered the activity of an intronic enhancer, with the variant allele linked to higher transcription activity and reduced 6-MP metabolism (lower TGN). By contrast, rs72846714 was not located in a regulatory element and instead its association signal was explained by linkage disequilibrium with a proximal functional variant rs12256506 that activatedNT5C2transcription in-cis. Our results indicated thatNT5C2germline variation significantly contributes to inter-patient variability in thiopurine drug disposition.
Simple rapidin vitroscreening method for SARS-CoV-2 anti-virals that identifies potential cytomorbidity-associated false positives
Authors: Yan Kexin , Rawle Daniel J. , Le Thuy T.T. , Suhrbier Andreas
Published: October 2020

The international SARS-CoV-2 pandemic has resulted in an urgent need to identify new anti-viral drugs for treatment of COVID-19 patients. The initial step to identifying potential candidates usually involvesin vitroscreening. Here we describe a simple rapid bioassay for drug screening using Vero E6 cells and inhibition of cytopathic effects (CPE) measured using crystal violet staining. The assay clearly illustrated the anti-viral activity of remdesivir, a drug known to inhibit SARS-CoV-2 replication. A key refinement involves a simple growth assay to identify drug concentrations that cause cellular stress or “cytomorbidity”, as distinct from cytotoxicity or loss of viability. For instance, hydroxychloroquine shows anti-viral activity at concentrations that slow cell growth, arguing that its purportedin vitroanti-viral activity arises from non-specific impairment of cellular activities.
ThePolycombgroup protein MEDEA controls cell proliferation and embryonic patterning inArabidopsis
Authors: Simonini Sara , Bemer Marian , Bencivenga Stefano , Gagliardini Valeria , Pires Nuno D. , Desvoyes Bénédicte , van der Graaff Eric , Gutierrez Crisanto , Grossniklaus Ueli
Published: October 2020

Establishing the body plan of a multicellular organism relies on precisely orchestrated cell divisions coupled with pattern formation. In animals, cell proliferation and embryonic patterning are regulated byPolycombgroup (PcG) proteins that form various multisubunit complexes (Grossniklaus and Paro, 2014). The evolutionary conservedPolycombRepressive Complex 2 (PRC2) trimethylates histone H3 at lysine 27 (H3K27me3) and comes in different flavors in the model plantArabidopsis thaliana(Förderer et al., 2016; Grossniklaus and Paro, 2014). The histone methyltransferase MEDEA (MEA) is part of the FERTILIZATION INDEPENDENT SEED (FIS)-PRC2 required for seed development4. Although embryos derived frommeamutant egg cells show morphological abnormalities (Grossniklaus et al., 1998), defects in the development of the placenta-like endosperm are considered the main cause of seed abortion (Kinoshita et al., 1999; Scott et al., 1998), and a role of FIS-PRC2 in embryonic patterning was dismissed (Bouyer et al., 2011; Leroy et al., 2007). Here, we demonstrate that endosperm lackingMEAactivity sustains normal embryo development and that embryos derived frommeamutant eggs abort even in presence of a wild-type endosperm becauseMEAis required for embryonic patterning and cell lineage determination. We show that, similar to PcG proteins in mammals, MEA regulates embryonic growth by repressing the transcription of core cell cycle components. Our work demonstrates thatArabidopsisembryogenesis is under epigenetic control of maternally expressed PcG proteins, revealing that PRC2 was independently recruited to control embryonic cell proliferation and patterning in animals and plants.
Spike development inhibition in theftinmutant is associated with multiple phenotypes and regulated by multiple biological pathways
Authors: Zheng Yongsheng , Zhang Jinpeng , Liu Cheng , Zhang Han , Ji Xiajie , Wang Mumu , wang Hui , Zhang Rongzhi , Li Ruyu , Liu Weihua
Published: October 2020

Spike development of wheat line 3558M was strongly inhibited by low temperature stress in spring. Thefertile tiller inhibition(ftin) gene in the wheat line 3558M is associated with multiple phenotypes, including the production of fewer tillers, delayed floral transition, and death of the shoot apical meristem. We systematically investigated the genes and pathways underlying the differences using ITRAQ proteomics and RNA-sequencing technologies and found multiple biological pathways including to the cold acclimation pathway and multiple defence responses (e.g. reactive oxygen species-mediated hypersensitive response, salicylic acid-mediated systemic acquired resistance) are activated and led to tillers death of the wheat line 3558M under cold stress. Meanwhile, the cold acclimation pathway inhibited the SVP-SCO1-LFY flowering pathway and led to delayed floral transition. Particularly, two TaPIN proteins were significantly downregulated, and multiple auxin signalling genes were also differentially expressed. Knocking down the twoTaPINgenes using RNAi technology significantly reduced the tiller number. The cold stress inhibited the auxin transport to reduce the tillers of 3558M. Taken together, theftingene might be a cold-sensitive mutation and that is the cause of multiple biological pathways and phenotypic changes.
Social contact patterns among employees in 3 U.S. companies during early phases of the COVID-19 pandemic, April to June 2020
Authors: Kiti Moses C. , Aguolu Obianuju G. , Liu Carol Y. , Mesa Ana R. , Regina Rachel , Willebrand Kathryn , Couzens Chandra , Bartelsmeyer Tilman , Nelson Kristin , Jenness Samuel , Riley Steven , Melegaro Alessia , Ahmed Faruque , Malik Fauzia , Lopman Ben , Omer Saad B.
Published: October 2020

2.

Importance

Devising control strategies against diseases such as COVID-19 require understanding of contextual social mixing and contact patterns. There has been no standardized multi-site social contact study conducted in workplace settings in the United States that can be used to broadly inform pandemic preparedness policy in these settings.

Objective

The study aimed to characterize the patterns of social contacts and mixing across workplace environments, including on-site or when teleworking.

Design

This was a cross-sectional non-probability survey that used standardized social contact diaries to collect data. Employees were requested to record their physical and non-physical contacts in a diary over two consecutive days, documented at the end of each day. Employees from each company were enrolled through email and electronic diaries sent as individual links. Data were collected from April to June 2020.

Setting

Two multinational consulting companies and one university administrative department, all located in Georgia, USA.

Participants

Employees opted into the study by accepting the invitation on a link sent via email.

Main Outcome

The outcome was median number of contacts per person per day. This was stratified by day of data collection, age, sex, race and ethnicity.

Results

Of 3,835 employees approached, 357 (9.3%) completed the first day of contact diary of which 304 completed both days of contact diary. There was a median of 2 contacts (IQR: 1-4, range: 0-21) per respondent on both day one and two. The majority (55%) of contacts involved conversation only, occurred at home (64%), and cumulatively lasted more than 4 hours (38%). Most contacts were repeated, and within same age groups, though participants aged 30-59 years reported substantial inter-generational mixing with children.

Conclusion

Participating employees in 3 surveyed workplaces reported few contacts, similar to studies from the UK and China when shelter-in-place orders were in effect during the pandemic. Many contacts were repeated which may limit the spread of infection. Future rounds are planned to assess changes in contact patterns when employees resume work in the office after the lockdown due to COVID-19 pandemic.
The global burden of yellow fever
Authors: Gaythorpe Katy A. M. , Hamlet Arran T. P. , Jean Kevin , Ramos Daniel Garkauskas , Cibrelus Laurence , Garske Tini , Ferguson Neil M.
Published: October 2020

Background

Yellow fever (YF) is a viral haemorrhagic fever endemic in tropical regions of Africa and South America. Current intervention policies, namely the Eliminate Yellow fever Epidemics (EYE) strategy are actioned through vaccination. However, the stockpiles and production mean that vaccination can be in short supply. As such, intervention strategies need to be optimised; one of the tools for doing this is mathematical modelling.

Methods

We fit a generalised linear model of YF reports to occurrence data available from 1987 to 2019 in Africa and South America and available serology survey data to estimate the force of infection across the continents. Then, using demographic and vaccination data, we examine the impact of interventions.

Findings

We estimate that in 2018 there were approximately 51,000 (95%CrI [31,000 - 82,000]) deaths due to YF in Africa and South America. When we examine the impact of mass vaccination campaigns in Africa, these amount to approximately 10,000 (95%CrI [6,000 - 17,000]) deaths averted in 2018 due to mass vaccination activities in Africa; this corresponds to a 47% reduction (95%CrI [10% - 77%]).

Interpretation

We find that the majority, 92% (95%CrI [89% - 95%]), of global burden occurs in Africa and that mass vaccination activities have significantly reduced the current deaths per year due to YF. This methodology allows us to evaluate the effectiveness of vaccination campaigns past, present and future and illustrates the need for continued vigilance and surveillance of YF.

Funding

BMGF and MRC