bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone
Authors: Fozouni Parinaz , Son Sungmin , de León Derby María Díaz , Knott Gavin J. , Gray Carley N. , D’Ambrosio Michael V. , Zhao Chunyu , Switz Neil A. , Kumar G. Renuka , Stephens Stephanie I. , Boehm Daniela , Tsou Chia-Lin , Shu Jeffrey , Bhuiya Abdul , Armstrong Max , Harris Andrew , Osterloh Jeannette M. , Meyer-Franke Anke , Langelier Charles , Pollard Katherine S. , Crawford Emily D. , Puschnik Andreas S. , Phelps Maira , Kistler Amy , DeRisi Joseph L. , Doudna Jennifer A. , Fletcher Daniel A. , Ott Melanie
Published: October 2020

The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic and pre-symptomatic carriers of the virus. CRISPR-based diagnostics that utilize RNA and DNA-targeting enzymes can augment gold-standard PCR-based testing if they can be made rapid, portable and accurate. Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. The assay achieved ∼100 copies/μL sensitivity in under 30 minutes and accurately detected a set of positive clinical samples in under 5 minutes. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity, and we directly quantified viral load using enzyme kinetics. Combined with mobile phone-based quantification, this assay can provide rapid, low-cost, point-of-care screening to aid in the control of SARS-CoV-2.
SARS-CoV-2 viral load peaks prior to symptom onset: a systematic review and individual-pooled analysis of coronavirus viral load from 66 studies
Authors: Benefield Amy E. , Skrip Laura A. , Clement Andrea , Althouse Rachel A. , Chang Stewart , Althouse Benjamin M.
Published: October 2020

Background

Since the emergence of COVID-19, tens of millions of people have been infected, and the global death toll approached 1 million by September 2020. Understanding the transmission dynamics of emerging pathogens, such as SARS-CoV-2 and other novel human coronaviruses is imperative in designing effective control measures. Viral load contributes to the transmission potential of the virus, but findings around the temporal viral load dynamics, particularly the peak of transmission potential, remain inconsistent across studies due to limited sample sizes.

Methods

We searched PubMed through June 8th 2020 and collated unique individual-patient data (IPD) from papers reporting temporal viral load and shedding data from coronaviruses in adherence with the PRISMA-IPD guidelines. We analyzed viral load trajectories using a series of generalized additive models and analyzed the duration of viral shedding by fitting log-normal models accounting for interval censoring.

Results

We identified 115 relevant papers and obtained data from 66 (57.4%) – representing a total of 1198 patients across 14 countries. SARS-CoV-2 viral load peaks prior to symptom onset and remains elevated for up to three weeks, while MERS-CoV and SARS-CoV viral loads peak after symptom onset. SARS-CoV-2, MERS-CoV, and SARS-CoV had median viral shedding durations of 4.8, 4.2, and 1.2 days after symptom onset. Disease severity, age, and specimen type all have an effect on viral load, but sex does not.

Discussion

Using a pooled analysis of the largest collection of IPD on viral load to date, we are the first to report that SARS-CoV-2 viral load peaks prior to – not at – symptom onset. Detailed estimation of the trajectories of viral load and virus shedding can inform the transmission, mathematical modeling, and clinical implications of SARS-CoV-2, MERS-CoV, and SARS-CoV infection.
Covid-19 related deaths among doctors in India
Authors: Kapoor Aanandita , Kapoor Krishan Mohan
Published: October 2020

Background

India has the most number of COVID-19 cases in the world currently, second only to the USA. The COVID-19 pandemic has caused high mortality not only in patients but also health care providers. In this paper, our aim is to analyze the cases of deaths in Indian doctors due to COVID-19 infection.

Methods

The details of data were taken from the list of the deceased doctors in India due to COVID-19 infection, which was compiled by the Indian Medical Association (IMA), the top body of Indian doctors practicing modern allopathic medicine. The key data fields of age, specialty, and geographical location of the deceased doctors were extracted from the given list, and analysis was performed.

Results

A total of 382 COVID-related deaths and 2174 infections were reported amongst doctors in India till 10 September 2020, with a case fatality rate of 16.7% among Indian doctors, which was ten times the CFR of 1.7% in the general population. Among the practicing doctors, after excluding the resident doctors and house surgeons, the CFR was 36.4%, which is almost 22 times more than what was seen in general population of India. The average age of COVID-related deaths in Indian doctors was 60.8 years, with a median age of 60; 62% of deaths among doctors were in the above 60 years, age group. The maximum number of deceased doctors were amongst general practitioners 225(58.9%). Among the specialists, most deaths were seen in paediatricians 26(6.8%), medical specialists 24(6.3%), general surgeons 22(5.8%), obstetricians & gynecologists 16(4.2%), and anesthesiologists 14(3.7%). The highest COVID-19 related deaths in doctors were seen in the Indian states of Tamil Nadu, Karnataka, Andhra Pradesh, Gujarat and Maharashtra in that order.

Conclusions

The mortality rate is very high among doctors in India compared to the general population. The average age of COVID-19 related death was 60 years among doctors. General practitioners and 60 years+ doctors are at a much higher risk of mortality among the doctors. The states with the high number of COVID-19 cases in India, also had a higher number of doctor deaths.
Single-cell sequencing of the human midbrain reveals glial activation and a neuronal state specific to Parkinson’s disease
Authors: Smajić S. , Prada-Medina C. A. , Landoulsi Z. , Dietrich C. , Jarazo J. , Henck J. , Balachandran S. , Pachchek S. , Morris C. M. , Antony P. , Timmermann B. , Sauer S. , Schwamborn J. C. , May P. , Grünewald A. , Spielmann M.
Published: October 2020

Parkinson’s disease (PD) etiology is associated with genetic and environmental factors that lead to a loss of dopaminergic neurons. However, the functional interpretation of PD-associated risk variants and how other midbrain cells contribute to this neurodegenerative process are poorly understood. Here, we profiled >41,000 single-nuclei transcriptomes of postmortem midbrain tissue from 6 idiopathic PD (IPD) patients and 5 matched controls. We show that PD-risk variants are associated with glia- and neuron-specific gene expression patterns. Furthermore, Microglia and astrocytes presented IPD-specific cell proliferation and dysregulation of genes related to unfolded protein response and cytokine signalling. IPD-microglia revealed a specific pro-inflammatory trajectory. Finally, we discovered a neuronal cell cluster exclusively present in IPD midbrains characterized by CADPS2 overexpression and a high proportion of cycling cells. We conclude that elevated CADPS2 expression is specific to dysfunctional dopaminergic neurons, which have lost their dopaminergic identity and unsuccessful attempt to re-enter the cell cycle.
Forecasting Covid-19 Infections and Deaths Horizon in Egypt
Authors: Nosier Shereen , Salah Reham
Published: October 2020

The coronavirus Covid-19 pandemic is defining a global health crisis, which is the hugest challenge the world has faced since World War II. Accordingly, the global economy as well is facing the worst economic catastrophe since the 1930s Great Depression. The case in Egypt is similar to the rest of the world. Despite being threatened by GDP decline and income losses; the Egyptian government has reacted early to restrain the pandemic outbreak. By mid-March, many measures had been undertaken to contain the spread of the virus. More than three months after imposing them, Egypt began lifting many of the restrictions put in place to curb the spread of coronavirus. Predictions of the potential spread of Covid-19 based on time series Auto Regressive Integrated Moving Average (ARIMA) and econometric Autoregressive-Distributed Lag (ARDL) forecasting models are utilized in this paper for designing and/or evaluating countermeasures. The aim of this study is threefold, first using the most recent available data to find the best prediction models for daily cases and death in Egypt and forecast them up to 7 November 2020. Second, to analyze the effect of mobility on the incidence of the pandemic using Google Community Mobility Reports (GCMR) to evaluate the results of easing lockdown restrictions. Finally, providing some recommendations that may help lessen the spread of the virus and eradicate new deaths as possible. The results revealed that mobility of population is affecting the incidence of new cases of Covid-19 significantly over the period of the study. Additionally, the total number of infections on November 7 2020 is expected to reach 102,352 cases, while the total death toll is predicted to be 5,938 according to the most accurate methods of forecasting. Accordingly, in order to sustain the predicted flat pandemic curve, many restrictions must be continued and emergency mechanisms need to be considered. For instance, adhering to the precautions of social distancing advised by the health minister and the declared hygiene rules to ensure that infection is prevented or transmitted is necessary. Besides, being prepared with re-imposing lockdown strategies and health system support are essential among others. It should also be noted that this expected pattern can shift, yet that depends on people’s actions.
A role for circular code properties in translation
Authors: Giannerini Simone , Danielli Alberto , Gonzalez Diego Luis , Goracci Greta
Published: October 2020

Circular codes represent a form of coding allowing detection/correction of frameshift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein expression levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results provide promising universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process.
Control of Vein-Forming, Striped Gene-Expression by Auxin Signaling
Authors: Krishna Anmol , Gardiner Jason , Donner Tyler J. , Scarpella Enrico
Published: October 2020

Activation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals, gene expression is activated in striped domains by the differential affinity of broadly expressed transcription factors for their target genes and the combinatorial interaction between such target genes. In plants, how gene expression is activated in striped domains is instead unknown. We address this question for the broadly expressed MONOPTEROS (MP) transcription factor and its target geneARABIDOPSIS THALIANA HOMEOBOX FACTOR8(ATHB8). We find thatATHB8promotes vein formation and that such vein-forming function depends on both levels ofATHB8expression and width ofATHB8expression domains. We further find thatATHB8expression is activated in striped domains by a combination of (1) activation ofATHB8expression through binding of peak levels of MP to a low-affinity MP-binding site in theATHB8promoter and (2) repression ofATHB8expression by MP target genes of theINDOLE-3-ACETIC-ACID-INDUCIBLEfamily such asBODENLOS. Our findings suggest that a common regulatory logic controls activation of gene expression in striped domains in both plants and animals despite the independent evolution of their multicellularity.
Mapping single-cell atlases throughout Metazoa unravels cell type evolution
Authors: Tarashansky Alexander J. , Musser Jacob M. , Khariton Margarita , Li Pengyang , Arendt Detlev , Quake Stephen R. , Wang Bo
Published: October 2020

Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories and diversifications in expression programs. Previously, we introduced the self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds from single-cell data (Tarashansky et al., 2019). Here, we build on SAM to map cell atlas manifolds across species. This new method, SAMap, identifies homologous cell types with shared expression programs across distant species within phyla, even in complex examples where homologous tissues emerge from distinct germ layers. SAMap also finds many genes with more similar expression to their paralogs than their orthologs, suggesting paralog substitution may be more common in evolution than previously appreciated. Lastly, comparing species across animal phyla, spanning mouse to sponge, reveals ancient contractile and stem cell families, which may have arisen early in animal evolution.
Clinical and genetic analysis of Costa Rican patients with Parkinson’s disease
Authors: Torrealba-Acosta Gabriel , Yu Eric , Lobo-Prada Tanya , Ruiz-Martínez Javier , Gorostidi-Pagola Ana , Gan-Or Ziv , Carazo-Céspedes Kenneth , Fornaguera-Trías Jaime
Published: October 2020

Background

Parkinson’s disease (PD) involves environmental risk and protective factors as well as genetic variance. Most of the research in genomics has been done in subjects of European ancestry leading to sampling bias and leaving Latin American populations underrepresented.

Objective

We sought to phenotype and genotype Costa Rican PD cases and controls.

Methods

We enrolled 118 PD patients with 97 unrelated controls. Collected information included demographics, exposure to risk and protective factors, motor and cognitive assessments. We sequenced coding and untranslated regions in familial PD and atypical parkinsonism-associated genes includingGBA, SNCA, VPS35, LRRK2, GCH1, PRKN, PINK1, DJ-1, VPS13C, ATP13A2.

Results

Mean age of PD probands was 62.12 ± 13.51 years, 57.6% were male. Prevalence of risk and protective factors reached 30%. Physical activity significantly correlated with better motor performance despite years of disease. Increased years of education were significantly associated with better cognitive function, whereas hallucinations, falls, mood disorders and coffee consumption correlated with worse cognitive performance. We did not identify an association between tested genes and PD or any damaging homozygous or compound heterozygous variants. Rare variants inLRRK2were nominally associated with PD, six were located between amino acids p.1620-1623 in the C-terminal-of-ROC (COR) domain of LRRK2. NonsynonymousGBAvariants (p.T369M, p.N370S, p.L444P) were identified in three healthy individuals. One PD patient carried a pathogenicGCH1variant, p.K224R.

Conclusion

This is the first study that reports on sociodemographic, risk factors, clinical presentation and genetics of Costa Rican patients with PD.
Spectrum of spinal cord involvement in COVID-19: A systematic review
Authors: Mondal Ritwick , Deb Shramana , Shome Gourav , Ganguly Upasana , Lahiri Durjoy , Leon Julian Benito
Published: October 2020

Background and aims

Recent reports reveal incidences of spinal cord involvement in form of para-infectious or post-infectious myelitis raising potential concerns about the possibilities of SARS-CoV-2 behind the pathogenesis of spinal cord demyelination. In this study, we intend to summarise so far available pieces of evidence documenting SARS-CoV-2 mediated spinal demyelination in terms of clinical, laboratory parameters and imaging characteristics.

Methodology

This review was carried out based on the existing PRISMA (Preferred Report for Systemic Review and Meta-analyses) consensus statement. Data was collected from four databases: Pubmed/Medline, NIH Litcovid, Embase and Cochrane library and Preprint servers up till 10th September, 2020. Search strategy comprised of a range of keywords from relevant medical subject headings which includes “SARS-COV-2”, “COVID-19”, “demyelination” etc.

Results

A total of 21 cases were included from 21 case reports after screening from various databases and preprint servers. Biochemical analysis reveals that the majority of cases showed elevated CSF protein as well as lymphocytic pleocytosis. Interestingly, a majority of cases were found to be associated with long extensive transverse myelitis (LETM), and remaining cases were found to be associated with isolated patchy involvement or isolated short segment involvement or combined LETM and patchy involvement. Few cases were also found with significant co-involvement of the brain and spine based on the imaging data.

Conclusion

It can be interpreted that SARS-CoV-2 may play a potential role in spinal demyelinating disorders in both para-infectious and post-infectious forms.

Highlights

Imaging data reveals LETM, short and patchy involvements

Para infectious myelitis precedes post-infectious manifestation

Altered CSF parameters and myelitis-like symptoms at the onset of COVID-19

Similar spinal cord involvements in related HCoVs infections
The effect of maternal pre-/early-pregnancy BMI and pregnancy smoking and alcohol on congenital heart diseases: a parental negative control study
Authors: Taylor Kurt , Elhakeem Ahmed , Nader Johanna Lucia Thorbjørnsrud , Yang Tiffany , Isaevska Elena , Richiardi Lorenzo , Vrijkotte Tanja , de Moira Angela Pinot , Murray Deirdre M , Finn Daragh , Mason Dan , Wright John , Oddie Sam , Roeleveld Nel , Harris Jennifer R , Andersen Anne-Marie Nybo , Caputo Massimo , Lawlor Deborah A.
Published: October 2020

Background

Congenital heart diseases (CHDs) are the most common congenital anomaly. The causes of CHDs are largely unknown, but intrauterine mechanisms appear to be important. Higher prenatal body mass index (BMI), smoking and alcohol consumption are associated with increased risk of CHDs. Whether these are causal is unclear.

Methods

Seven European birth cohorts including 232,390 offspring were included. We applied negative exposure paternal control analyses to explore the intrauterine effects of maternal BMI, smoking and alcohol consumption during pregnancy, on offspring CHDs and CHD severity. We used logistic regression and combined estimates using a fixed-effects meta-analysis and compared maternal-specific confounder-adjusted associations to similarly adjusted associations of paternal exposures. If there is a causal intrauterine effect of a maternal pregnancy exposure, we would expect to see a maternal-specific association, with no (or weaker) association with the paternal exposure.

Results

There were 2,469 CHD cases (1.1%). The association of mean BMI with CHD was null and similar in mothers (adjusted OR per 1kg/m2: 1.00 (95%CI: 0.99, 1.02)) and fathers (OR: 1.01 (0.99, 1.03)). The analyses of BMI categories resulted in similar increased odds of CHD in overweight (mothers OR: 1.15 (1.01, 1.31) and fathers 1.10 (0.96, 1.27)) and obesity (mothers OR: 1.12 (0.93, 1.36) and fathers 1.16 (0.90, 1.50)). Maternal smoking was associated with increased odds of CHD (OR: 1.11 (0.97, 1.25)) but paternal smoking was not (OR: 0.96 (0.85, 1.07)). The difference increased when removing offspring with genetic/chromosomal defects (mothers OR: 1.15 (1.01, 1.32) and fathers 0.93 (0.83, 1.05)). The positive association with maternal pregnancy smoking appeared to be driven by non-severe CHD cases (OR: 1.22 (1.04, 1.44)). Associations with maternal (OR: 1.16 (0.52, 2.58)) and paternal (OR: 1.23 (0.74, 2.06)) moderate/heavy pregnancy alcohol consumption were similar.

Conclusions

We have shown that maternal, but not paternal, pregnancy smoking is associated with an increase in odds of offspring CHDs, primarily non-severe CHDs, providing evidence of an intrauterine effect. We found no strong evidence of an intrauterine effect of higher maternal BMI or alcohol consumption on offspring CHDs. Our findings provide further evidence for why smoking cessation is important during pregnancy.
Identification of biological correlates associated with respiratory failure in COVID-19
Authors: Oh Jung Hun , Tannenbaum Allen , Deasy Joseph O
Published: October 2020

Background

Coronavirus disease 2019 (COVID-19) is a global public health concern. Recently, a genome-wide association study (GWAS) was performed with participants recruited from Italy and Spain by an international consortium group.

Methods

Summary GWAS statistics for 1610 patients with COVID-19 respiratory failure and 2205 controls were downloaded. In the current study, we analyzed the summary statistics with the information of loci and p-values for 8,582,968 single-nucleotide polymorphisms (SNPs), using gene ontology analysis to determine the top biological processes implicated in respiratory failure in COVID-19 patients.

Results

We considered the top 708 SNPs, using a p-value cutoff of 5×10−5, which were mapped to the nearest genes, leading to 144 unique genes. The list of genes was input into a curated database to conduct gene ontology and protein-protein interaction (PPI) analyses. The top ranked biological processes were wound healing, epithelial structure maintenance, muscle system processes, and cardiac-relevant biological processes with a false discovery rate < 0.05. In the PPI analysis, the largest connected network consisted of 8 genes. Through literature search, 7 out of the 8 genes were found to be implicated in both pulmonary and cardiac diseases.

Conclusion

Gene ontology and protein-protein interaction analyses identified cardio-pulmonary processes that may partially explain the risk of respiratory failure in COVID-19 patients.
Congruence of Health-related Quality of Life Assessment between Patient-Physician and Patient-Caregiver Dyads
Authors: Tang Chia-Chun , Chen Hsi , Wu Wei-Wen , Tsai Jaw-Shiun
Published: October 2020

Background

Exploring the congruence of health-related quality of life (HRQOL) evaluation provides valuable information regarding whether proxies can accurately reflect patient perceptions and the quality of symptom communication. It is particular important in advanced cancer population who experience poor HRQOL and have deteriorated ability to express their feeling. The main purpose of this study was to investigate the congruence of HRQOL reports between patient-physician and patient-caregiver dyads and to determine the association of variables, if any, with the congruence between dyads.

Methods

This observational study with a cross-sectional design first approached physicians who provided care for patients with advanced cancer at the participating institution. Then, participated physicians’ patients and their caregivers were recruited. All participants were required to independently fill out an HRQOL questionnaire during their outpatient visits. Descriptive statistics, weighted kappa, Wilcoxon signed-rank test, and linear regression were employed for data analysis.

Results

A total of 52 patient-physician and 27 patient-caregiver dyads were examined. Patients suffered from considerable problems in all three HRQOL domains: symptom, functioning, and overall HRQOL. The patients’ level of agreement was moderate with the caregivers and fair with the physicians. A significant relationship was found between several patient-related variables and disagreement.

Conclusion

The study’s patient group experienced a compromised HRQOL, warranting immediate attention. When there are barriers to obtaining a patient’s self-repot, clinicians may consider caregivers as reasonable source. Some patients with special characteristics may need additional attention because their problems may be at greater risk of being overlooked.
Chromoplast differentiation in bell pepper (Capsicum annuum) fruits
Authors: Rödiger Anja , Agne Birgit , Dobritzsch Dirk , Helm Stefan , Müller Fränze , Pötzsch Nina , Baginsky Sacha
Published: October 2020

We report here a detailed analysis of the proteome adjustments that accompany chromoplast differentiation from chloroplasts during bell-pepper fruit ripening. While the two photosystems are disassembled and their constituents degraded, the cytochrome b6f complex, the ATPase complex as well as Calvin cycle enzymes are maintained at high levels up to fully mature chromoplasts. This is also true for ferredoxin (Fd) and Fd-dependent NADP reductase, suggesting that ferredoxin retains a central role in the chromoplasts redox metabolism. There is a significant increase in the amount of enzymes of the typical metabolism of heterotrophic plastids such as the oxidative pentose phosphate pathway (OPPP), amino acid and fatty acid biosynthesis. Enzymes of chlorophyll catabolism and carotenoid biosynthesis increase in abundance, supporting the pigment reorganization that goes together with chromoplast differentiation. The majority of plastid encoded proteins declines but constituents of the plastid ribosome and AccD increase in abundance. Furthermore, the amount of plastid terminal oxidase (PTOX) remains unchanged despite a significant increase in phytoene desaturase (PDS) levels, suggesting that the electrons from phytoene desaturation may be consumed by another oxidase. This may be a particularity of non-climacteric fruits such as bell pepper, that lack a respiratory burst at the onset of fruit ripening.
Cryptic genetic variation in a heat shock protein shapes the expressivity of a mutation affecting stem cell behaviour inC. elegans
Authors: Koneru Sneha L. , Hintze Mark , Katsanos Dimitris , Barkoulas Michalis
Published: October 2020

A fundamental question in medical genetics is how the genetic background modifies the phenotypic outcome of key mutations. We address this question by focusing on the epidermal seam cells, which display stem cell properties inCaenorhabditis elegans. We demonstrate that a null mutation in the GATA transcription factoregl-18, which is involved in seam cell fate maintenance, is more tolerated and thus has lower expressivity in the divergent CB4856 isolate from Hawaii than the lab reference strain N2 from Bristol. We identify multiple quantitative trait loci (QTLs) underlying the difference in mutation expressivity between the two isolates. These QTLs reveal cryptic genetic variation, which acts to reinforce seam cell fate through potentiating Wnt signalling. Within one QTL region, a single amino acid deletion in the heat shock protein HSP-110 in CB4856 lowersegl-18mutation expressivity. Our work underscores that natural variation in conserved heat shock proteins can shape mutation expressivity.
Within-species floral odor variation is maintained by spatial and temporal heterogeneity in pollinator communities
Authors: Szenteczki Mark A. , Godschalx Adrienne L. , Galmán Andrea , Espíndola Anahí , Gibernau Marc , Alvarez Nadir , Rasmann Sergio
Published: October 2020

Floral odor is a complex trait that mediates many biotic interactions, including pollination. While high intraspecific floral odor variation appears to be common, the ecological and evolutionary drivers of this variation are often unclear. Here, we investigated the influence of spatially and temporally heterogeneous pollinator communities on floral odor variation inArum maculatum(Araceae). Through Europe-wide field surveys, we identified high floral odor diversity and shifts in the dominant pollinator species within severalA. maculatumpopulations compared to pollinator data from the same sites ten years ago. Using common-garden experiments, we further confirmed that inflorescences from native and foreign pollinator backgrounds were equally efficient at attracting local pollinators. The substantial within-population floral odor variation we observed may therefore be advantageous when facing temporally heterogeneous pollinator communities. We propose spatio-temporal heterogeneity in pollinators as one potential mechanism maintaining diverse floral odor bouquets in angiosperms.
Hippocampal silent infarct leads to subtle cognitive decline that is associated with inflammation and gliosis at twenty-four hours after injury in a rat model
Authors: Finney Caitlin A. , Morris Margaret J. , Westbrook R. Frederick , Jones Nicole M.
Published: October 2020

Silent infarcts (SI) are subcortical cerebral infarcts that occur in the absence of clinical symptoms commonly associated with ischemia and are linked to dementia development. Little is known about the pathophysiology underlying the cognitive dysfunction associated with SI, and few studies have examined the early cellular responses and neurobiological underpinnings. We induced SI in adult male Sprague-Dawley rats using an infusion of endothelin-1 in the CA1 dorsal hippocampus. Twenty-four hours later, we assessed cognition using the hippocampal-dependent object place recognition task. We also examined whether the resulting cognitive effects were associated with common markers of ischemia, specifically cell and synapse loss, gliosis, and inflammation, using histology and immunohistochemistry. Hippocampal SI led to subtle cognitive impairment on the object place recognition task 24-hours post-injury. This was characterized by a significant difference in exploration proportion relative to a pre-injury baseline and a positive association between time spent with both the moved and unmoved objects. SI did not result in any detectable cell or synaptophysin loss, but did increase apoptosis, gliosis and inflammation in the CA1. Principal component analysis indicated the main variables associated with hippocampal SI included increased time spent with the unmoved object, gliosis, apoptosis and inflammation as well as decreased exploration proportion and CA1 cells. Our data demonstrate that hippocampal SI can lead to cognitive dysfunction 24-hours after injury. Further, this appears to be driven by early degenerative processes including apoptosis, gliosis and inflammation, suggesting that these may be targets for early interventions treating hippocampal SI and its cognitive consequences.
Dynamics of brain function in chronic pain patients assessed by microstate analysis of resting-state electroencephalography
Authors: May Elisabeth S. , Gil Ávila Cristina , Dinh Son Ta , Heitmann Henrik , Hohn Vanessa D. , Nickel Moritz M. , Tiemann Laura , Tölle Thomas R. , Ploner Markus
Published: October 2020

Chronic pain is a highly prevalent and severely disabling disease, which is associated with substantial changes of brain function. Such changes have mostly been observed when analyzing static measures of brain activity during the resting-state. However, brain activity varies over time and it is increasingly recognized that the temporal dynamics of brain activity provide behaviorally relevant information in different neuropsychiatric disorders. Here, we therefore investigated whether the temporal dynamics of brain function are altered in chronic pain. To this end, we applied microstate analysis to eyes-open and eyes-closed resting-state electroencephalography (EEG) data of 101 patients suffering from chronic pain and 88 age- and gender-matched healthy controls. Microstate analysis describes EEG activity as a sequence of a limited number of topographies termed microstates, which remain stable for tens of milliseconds. Our results revealed that sequences of 5 microstates, labelled with the letters A to E, described resting-state brain activity in both groups and conditions. Bayesian analysis of the temporal characteristics of microstates revealed that microstate D has a less predominant role in patients than in healthy participants. This difference was consistently found in eyes-open and eyes-closed EEG recordings. No evidence for differences in other microstates was found. As microstate D has been previously related to attentional networks and functions, abnormalities of microstate D might relate to dysfunctional attentional processes in chronic pain. These findings add to the understanding of the pathophysiology of chronic pain and might eventually contribute to the development of an EEG-based biomarker of chronic pain.
Jasmonate biosynthesis arising from altered cell walls is prompted by turgor-driven mechanical compression and guides root hydrotropism
Authors: Mielke Stefan , Zimmer Marlene , Meena Mukesh Kumar , Dreos René , Stellmach Hagen , Hause Bettina , Voiniciuc Cătălin , Gasperini Debora
Published: October 2020

Despite the vital roles of jasmonoyl-isoleucine (JA-Ile) in governing plant growth and environmental acclimation, it remains unclear what intracellular processes lead to its induction. Here, we provide compelling genetic evidence that mechanical and osmotic regulation of turgor pressure represents a key factor in eliciting JA-Ile biosynthesis. After identifying cell wall mutant alleles inKORRIGAN1(KOR1) with elevated JA-Ile in seedling roots, we found that ectopic JA-Ile resulted from cell non-autonomous signals deriving from enlarged cortex cells compressing inner tissues and stimulating JA-Ile production. Restoring cortex cell size by cell-type-specific KOR1 complementation, by isolating a genetickor1suppressor, and by lowering turgor pressure with hyperosmotic treatments, abolished JA-Ile signalling. Strikingly, heightened JA-Ile levels guidedkor1roots towards greater water availability, uncovering a previously unrecognized JA-Ile function in root hydrotropism. Collectively, these findings enhance our understanding of JA-Ile biosynthesis initiation, and reveal a novel role of JA-Ile in orchestrating environmental resilience.
Transcriptome and interactome analyses identify theTP53interacting geneRCCD1as a candidate susceptibility gene at the 15p26.1 breast and ovarian cancer risk locus
Authors: Plummer Jasmine , Dezem Felipe Segato , Chen Stephanie S. , Dhungana Subash , Wali Deepika , Davis Brian , Kanska Justyna , Safi Niko , Seo Ji-Heui , Corona Rosario I , Schildkraut Joellen M , Pharoah Paul DP , Lawrenson Kate , Knott Simon RV , Freedman Matthew L , Kar Siddhartha P , Gayther Simon A
Published: October 2020

Common genetic variation in a region on chromosome 15q26 confers susceptibility to breast and ovarian cancer. The P53 interacting gene RCCD1 in this region is a candidate susceptibility gene for both cancers. In this study, a colocalization analysis of breast and ovarian cancer case-control genetic association studies in over 145,000 and 146,000 controls fine mapped the shared association in this region to 17 pleiotropic credible causal risk variants (Pbreast< 1.16 × 10−14andPovary< 7.50 × 10−7). These variants were strongly associated with the expression of RCCD1 in normal breast and ovarian tissues. Circular chromosome conformation capture (4C) analysis ofRCCD1in breast and ovarian cancer cells identified similar patterns ofcis-interaction and significant binding site enrichment for theBRCA2interacting geneEMSY(Padjusted= 9.24 × 10−6). The 4C analysis pinpointed a single 2kB RCCD1 cis-interaction that contained two of the 17 shared risk variants. RCCD1trans-interacting regions mapped to previously identified genome wide significant (P < 5 × 10−8) breast cancer risk loci (1p34.2 and 3p14.1) and to the pleiotropic breast-ovarian cancer risk locus at chromosome 9q34.2. Stable overexpression of RCCD1 in breast and ovarian cancer precursor cells identified 13 and 11 differentially expressed genes (DEGs) respectively associated with breast and ovarian cancer risk at genome-wide significance (PMAGMA< 2.6 × 10−6after Bonferroni correction). Eighty-two DEGs shared between breast and ovarian cancer were strongly enriched in TP53 (P = 9.9 × 10−4), Hippo (P = 2.51 × 10−3) and TNF signaling (P = 4.7 × 10−3) pathways.
Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers
Authors: Rosenke Kyle , Leventhal Shanna , Moulton Hong M. , Hatlevig Susan , Hawman David , Feldmann Heinz , Stein David A.
Published: October 2020

Synopsis

Background

SARS-CoV-2 is the causative agent of COVID-19 and a pathogen of immense global public health importance. Development of innovative direct-acting antiviral agents is sorely needed to address this virus. Peptide-conjugated morpholino oligomers (PPMO) are antisense agents composed of a phosphordiamidate morpholino oligomer covalently conjugated to a cell-penetrating peptide. PPMO require no delivery assistance to enter cells and are able to reduce expression of targeted RNA through sequence-specific steric blocking.

Objectives and Methods

Five PPMO designed against sequences of genomic RNA in the SARS-CoV-2 5’-untranslated region and a negative control PPMO of random sequence were synthesized. Each PPMO was evaluated for its effect on the viability of uninfected cells and its inhibitory effect on the replication of SARS-CoV-2 in Vero-E6 cell cultures. Cell viability was evaluated with an ATP-based method and viral growth was measured with quantitative RT-PCR and TCID50infectivity assays.

Results

PPMO designed to base-pair with sequence in the 5’-terminal region or the leader transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, in a non-toxic and dose-responsive manner.

Conclusion

The data indicate that PPMO have the ability to potently and specifically suppress SARS-CoV-2 growth and are promising candidates for further pre-clinical development.
A Genome-wide microRNA screen identifies the microRNA-183/96/182 cluster as a modulator of circadian rhythms
Authors: Zhou Lili , Miller Caitlyn , Miraglia Loren J. , Romero Angelica , Mure Ludovic S. , Panda Satchidananda , Kay Steve A.
Published: October 2020

The regulatory mechanisms of circadian rhythms have been studied primarily at the level of the transcription-translation feedback loops of protein coding genes. Regulatory modules involving non-coding RNAs are less thoroughly understood. In particular, emerging evidence has revealed the important role of miRNAs in maintaining the robustness of the circadian system. To identify miRNAs that have the potential to modulate circadian rhythms, we conducted a genome-wide miRNA screen using U2OS luciferase reporter cells. Among 989 miRNAs in the library, 120 changed the period length in a dosage-dependent manner. We further validated the circadian regulatory function of a miRNA cluster, miR-183/96/182, bothin vitroandin vivo. We found that all three members of this miRNA cluster can modulate circadian rhythms. Particularly, miR-96 directly targeted a core circadian clock gene, PER2. The knockout of the miR-183/96/182 cluster in mice showed tissue-specific effects on circadian parameters and altered circadian rhythms at the behavioral level. This study identified a large number of miRNAs, including the miR-183/96/182 cluster, as circadian modulators. We provide a resource for further understanding the role of miRNAs in the circadian network and highlight the importance of miRNAs as a novel genome-wide layer of circadian clock regulation.

Significance Statement

Although miRNAs are emerging as important regulators of diverse physiological and pathological processes, our knowledge of their potential role in regulation of circadian rhythms is still limited. We deployed a cell-based genome-wide screening approach, and successfully identified mature miRNAs as cell-autonomous circadian modulators. We then specifically focused on the miR-183/96/182 cluster among the candidate miRNA hits and revealed their circadian function bothin vitroand invivofrom the unbiased screen. This study provides resources for further understanding the role of miRNAs in the circadian network. It also highlights the importance of miRNAs as a novel genome-wide layer of circadian clock regulation.
Effects of N-linked glycan of Lassa Virus Envelope Glycoprotein on the Immune Response
Authors: Zhu Xueqin , Liu Yang , Guo Jiao , Wang Zonglin , Cao Junyuan , Xiao Gengfu , Wang Wei
Published: October 2020

Lassa virus (LASV) belongs to theMammarenavirusgenus (family Arenaviridae) and causes severe hemorrhagic fever in humans. The glycoprotein precursor (GPC) contains eleven N-linked glycans that play essential roles in GPC functionalities such as cleavage, transport, receptor recognition, epitope shielding, and immune response. We used three mutagenesis strategies to abolish the individual glycan chains on the GPC and found that all three mutations led to cleavage inefficiency on the 2nd, 5th, and 8thglycosylation motifs. To evaluate N to Q mutagenesis for further research, it was found that deletion of the 2ndand 8thglycans completely inhibited the infectivity. We further investigated the role of glycans on GPC-mediated immune response by DNA immunization of mice. Deletion of the individual 1st, 3rd, 5thand 6thglycans significantly enhanced the proportion of effector CD4+ cells, whereas deletion of the 1st, 2nd, 3rd, 4th5th, 6th, and 9thglycans enhanced the proportion of CD8+ effector T cells. Deletion of specific glycans improves the Th1-type immune response, and abolishment of glycan on GPC generally increases the antibody titer to the glycan-deficient GPC. However, the antibodies from either the mutant or WT GPC-immunized mice show little neutralization effect on wild-type LASV. The glycan residues on GPC provide an immune shield for the virus, and thus represent a target for the design and development of a vaccine.

Importance

At present, there are no Food and Drug Administration-approved drugs or vaccines specific for LASV. Similar to other enveloped viruses with a heavy glycan shield, the N-linked glycans of LASV make it difficult for effector T cells and neutralization antibodies to access the glycoprotein epitope. In this study, we evaluated the effect of the individual glycan chains on GPC-mediated immune response, and found that deletion of the glycan improves the proportion of effector T cells, improving the Th1-type immune response, and increasing the antibody titer to the WT and mutant GPC, which may be beneficial to vaccine design and development.
Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test
Authors: Bal Antonin , Pozzetto Bruno , Trabaud Mary-Anne , Escuret Vanessa , Rabilloud Muriel , Langlois-Jacques Carole , Paul Adèle , Guibert Nicolas , D’Aubarede Constance , Massardier-Pilonchery Amélie , Boibieux André , Morfin Florence , Pitiot Virginie , Gueyffier François , Lina Bruno , Fassier Jean-Baptiste , Trouillet-Assant Sophie ,   COVID SER STUDY GROUP
Published: October 2020

Objectives

We evaluated widely-used SARS-CoV-2 serological tests and their potential association with virus neutralization test (VNT) in a cohort of mild COVID-19 patients.

Methods

A total of 439 specimens were longitudinally collected from 76 healthcare workers with RT-PCR-confirmed mild COVID-19. Nine serological assays developed by leading global companies (Abbott, DiaSorin, Siemens, Bio-Rad, Wantai, bioMérieux, Euroimmun) were assessed. For each test the sensitivity to detect SARS-CoV-2 antibodies was determined weekly after symptom onset. Correlation and concordance were assessed using the Spearman and Cohen’s Kappa coefficients, respectively. Positive percent agreement and negative percent agreement (NPA) with the VNT were also determined.

Results

The Wantai Total Ab assay targeting the receptor binding domain (RBD) within the S protein presented the best sensitivity at different times during the course of disease. The best correlation between antibody level and neutralizing antibody titer was found with the Euroimmun S1-based IgA assay (Spearman coefficient [95%CI]: 0.71 [0.61-0.79]). A moderate concordance (Kappa [95%CI]: 0.43[0.23-0.63]) as well as the lowest NPA (33%) was found between the Wantai Total Ab assay and the VNT. Compared to the Wantai Total Ab assay, other total Ab or IgG assays targeting the S or the RBD (bioMérieux, DiaSorin, Siemens,) were more concordant with the VNT (Kappa>0.7 for the three tests) and had a higher NPA (range: 90% to 97%).

Conclusions

Although some assays presented a better concordance with VNT than others, the present findings emphasize that commercialized serological tests including those targeting the RBD cannot substitute VNT for the assessment of functional antibody response.
An integrated clinical and genetic model for predicting risk of severe COVID-19
Authors: Dite Gillian S. , Murphy Nicholas M. , Allman Richard
Published: October 2020

Background

Age and gender are often the only considerations in determining risk of severe COVID-19. There is an urgent need for accurate prediction of the risk of severe COVID-19 for use in workplaces and healthcare settings, and for individual risk management.

Methods

Clinical risk factors and a panel of 64 single-nucleotide polymorphisms were identified from published data. We used logistic regression to develop a model for severe COVID-19 in 1,582 UK Biobank participants aged 50 years and over who tested positive for the SARS-CoV-2 virus: 1,018 with severe disease and 564 without severe disease. Model discrimination was assessed using the area under the receiver operating characteristic curve (AUC).

Results

A model incorporating the SNP score and clinical risk factors (AUC=0.786) had 111% better discrimination of disease severity than a model with just age and gender (AUC=0.635). The effects of age and gender are attenuated by the other risk factors, suggesting that it is those risk factors – not age and gender – that confer risk of severe disease. In the whole UK Biobank, most are at low or only slightly elevated risk, but one- third are at two-fold or more increased risk.

Conclusions

We have developed a model that enables accurate prediction of severe COVID-19. Continuing to rely on age and gender alone to determine risk of severe COVID-19 will unnecessarily classify healthy older people as being at high risk and will fail to accurately quantify the increased risk for younger people with comorbidities.