bluuebunny/crossref_metadata_2025 huggingface dataset:
"Even though I am alone, I feel that we are many" - An appreciative inquiry study of asynchronous, provider-to-provider teleconsultations in Turkana, Kenya
Authors: Fry M Whitney , Saidi Salima , Musa Abdirahman , Kithyoma Vanessa , Kumar Pratap
Published: May 2020

Non-physician clinicians (NPCs) in low and middle-income countries (LMICs) often have little physical proximity to the resources - equipment, supplies or skills - needed to deliver effective care, forcing them to refer patients to distant sites. Unlike equipment or supplies, which require dedicated supply chains, physician/specialist skills needed to support NPCs can be sourced and delivered through telecommunication technologies. In LMICs however, these skills are scarce and sparsely distributed, making it difficult to implement commonly used real-time (synchronous), hub-and-spoke telemedicine paradigms. An asynchronous teleconsultations service was implemented in Turkana County, Kenya, connecting NPCs with a volunteer network of remote physicians and specialists. In 2017-18, the service supported over 100 teleconsultations and referrals across 20 primary healthcare clinics and two hospitals. This qualitative study aimed to explore the impact of the telemedicine intervention on health system stakeholders, and perceived health-related benefits to patients. Data were collected using Appreciative Inquiry, a strengths-based, positive approach to assessing interventions and informing systems change. We highlight the impact of provider-to-provider asynchronous teleconsultations on multiple stakeholders and healthcare processes. Provider benefits include improved communication and team work, increased confidence and capacity to deliver services in remote sites, and professional satisfaction for both NPCs and remote physicians. Health system benefits include efficiency improvements through improved care coordination and avoiding unnecessary referrals, and increased equity and access to physician/specialist care by reducing geographical, financial and social barriers. Providers and health system managers recognised several non-health benefits to patients including increased trust and care seeking from NPCs, and social benefits of avoiding unnecessary referrals (reduced social disruption, displacement and costs). The findings reveal the wider impact that modern teleconsultation services enabled by mobile technologies and algorithms can have on LMIC communities and health systems. The study highlights the importance of viewing provider-to-provider teleconsultations as complex health service delivery interventions with multiple pathways and processes that can ultimately improve health outcomes.
Will an imperfect vaccine curtail the COVID-19 pandemic in the U.S.?
Authors: Iboi Enahoro Amos , Ngonghala Calistus N. , Gumel Abba B
Published: May 2020

The novel coronavirus (COVID-19) that emerged from Wuhan city of China in late December 2019 continue to pose devastating public health and economic challenges across the world. Although the community-wide implementation of basic non-pharmaceutical intervention measures, such as social-distancing, quarantine of suspected COVID-19 cases, isolation of confirmed cases, use of face masks in public, and contact-tracing, have been quite effective in curtailing and mitigating the burden of the pandemic, it is universally believed that the use of an anti-COVID-19 vaccine is necessary to build the community herd immunity needed to effectively control and eliminate the pandemic. This study is based on the design and use of a mathematical model for assessing the population-level impact of a hypothetical imperfect anti-COVID-19 vaccine on the control of COVID-19. An analytical expression for the minimum number of unvaccinated susceptible individuals needed to be vaccinated to achieve vaccine-induced community herd immunity is derived. The epidemiological consequence of the herd immunity threshold is that the disease can be effectively controlled or eliminated if the minimum herd immunity threshold is achieved in the community. Simulations of the model, using baseline parameter values obtained from fitting the model with mortality data relevant to COVID-19 dynamics in the US states of New York and Florida, as well as for the entire US, show that, for an anti-COVID-19 vaccine with an assumed protective efficacy of 80%, the minimum herd immunity threshold for the entire US, state of New York and state of Florida are, respectively, 90%, 84% and 85%. Furthermore, it was shown that, while a significantly large increase in vaccination rate (from baseline) is necessarily needed to eliminate COVID-19 from the entire US, the pandemic can be eliminated from the states of New York and Florida if the vaccination rate is marginally increased (by as low as 10%) from its baseline value.
The prospect of COVID-19 elimination in the US or in the two states of New York and Florida is greatly enhanced if the vaccination program is combined with a public mask use program or an effective social-distancing measure. Such combination of strategies significantly reduces the vaccine-induced herd immunity threshold. Finally, it is shown that the vaccination program is more likely to lead to COVID-19 elimination in the state of Florida, followed by the state of New York and then the entire US.
The far side of the COVID-19 epidemic curve: local re-openings and re-closings based on globally coordinated triggers may work best
Authors: Karatayev Vadim A. , Anand Madhur , Bauch Chris T.
Published: May 2020

In the late stages of an epidemic, infections are often sporadic and geographically distributed. Spatially structured stochastic models can capture these important features of disease dynamics, thereby allowing a broader exploration of interventions. Here we develop a stochastic model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission amongst an interconnected group of population centres representing counties, municipalities and districts (collectively, “counties”). The model is parameterized with demographic, epidemiological, testing, and travel data from Ontario, Canada. We explore the effects of different control strategies after the epidemic curve has been flattened. We compare a local strategy of re-opening (and re-closing, as needed) schools and workplaces county-by-county according to triggers for county-specific infection prevalence, to a global strategy of province-wide re-opening and re-closing according to triggers for province-wide infection prevalence. We find that the local strategy results in a similar number coronavirus disease (COVID-19) cases but significantly fewer person-days of closure, even under high inter-county travel scenarios. However, both cases and person-days lost to closure rise when county triggers are not coordinated and when testing rates vary among counties. Finally, we show that local strategies can also do better in the early epidemic stage but only if testing rates are high and the trigger prevalence is low. Our results suggest that pandemic planning for the far side of the COVID-19 epidemic curve should consider local strategies for re-opening and re-closing.
Spread of COVID-19 in India: A Simple Algebraic Study
Authors: Roy Sudipto
Published: May 2020

The number of patients, infected with COVID-19, began to increase very rapidly in India from March 2020. The country was put under lockdown from 25 March 2020. The present study is aimed at providing a simple algebraic analysis of the trend that is evident in the spread of the disease in this part of the world. The purpose of this algebraic approach is to simplify the calculation sufficiently by deviating from the standard techniques that are conventionally used to construct mathematical models of epidemics. The predictions, obtained from this algebraic study, are found to be in reasonable agreement with the recorded data. Using this mathematical formulation we have determined the time variation of the number of asymptomatic patients, who are believed to play a major role in spreading the disease. We have discussed the effect of lockdown in reducing the rate of transmission of the disease. On the basis of the proposed models, predictions have been made regarding the possible trend of the rise in the number of cases beyond the withdrawal of lockdown. All these things have been calculated by using very simple mathematical expressions which can be easily understood and used by those who have a rudimentary knowledge of algebra.
Identification of antigen-specific TCR sequences using a strategy based on biological and statistical enrichment in unselected subjects
Authors: Smith Neal P. , Ruiter Bert , Virkud Yamini V. , Shreffler Wayne G.
Published: May 2020

Recent advances in high-throughput T cell receptor (TCR) sequencing have allowed for new insights into the TCR repertoire. However, methods for capturing antigen-specific repertoires remain an area of development. Here, we describe a novel approach that utilizes both a biological and statistical enrichment to define putatively antigen-specific complementarity-determining region 3 (CDR3) repertoires in unrelated individuals. The biological enrichment entails fluorescence-activated cell sorting ofin vitroantigen-activated memory CD4+T cells followed by TCRβ sequencing. The resulting TCRβ sequences are then filtered by selecting those that are statistically enriched when compared to their frequency in the autologous resting T cell compartment. Applying this method to define putatively peanut protein-specific repertoires in 27 peanut-allergic individuals resulted in a library of 7345 unique CDR3 amino acid sequences that had similar characteristics to validated antigen-specific repertoires in terms of homology and diversity. In-depth analysis of these CDR3s revealed 36 public sequences that demonstrated high levels of convergent recombination. In a network analysis, the public CDR3s unveiled themselves as core sequences with more edges than their private counterparts. This method has the potential to be applied to a wide range of T cell mediated disorders, and to yield new biomarkers and biological insights.
Metabolic engineering ofEscherichia colifor optimized biosynthesis of nicotinamide mononucleotide, a noncanonical redox cofactor
Authors: Black William B. , Aspacio Derek , Bever Danielle , King Edward , Zhang Linyue , Li Han
Published: May 2020

Background

Noncanonical redox cofactors are emerging as important tools in cell-free biosynthesis to increase the economic viability, to enable exquisite control, and to expand the range of chemistries accessible. However, these noncanonical redox cofactors need to be biologically synthesized to achieve full integration with renewable biomanufacturing processes.

Results

In this work, we engineeredEscherichia colicells to biosynthesize the noncanonical cofactor nicotinamide mononucleotide (NMN+), which has been efficiently used in cell-free biosynthesis. First, we developed a growth-based screening platform to identify effective NMN+biosynthetic pathways inE. coli. Second, we explored various pathway combinations and host gene disruption to achieve an intracellular level of ~1.5 mM NMN+, a 130-fold increase over the cell’s basal level, in the best strain, which features a previously uncharacterized nicotinamide phosphoribosyltransferase (NadV) fromRalstonia solanacearum.Last, we revealed mechanisms through which NMN+accumulation impactsE. colicell fitness, which sheds light on future work aiming to improve the production of this noncanonical redox cofactor.

Conclusion

These results further the understanding of effective production and integration of NMN+intoE. coli. This may enable the implementation of NMN+-directed biocatalysis without the need for exogenous cofactor supply.
Protection from α-synuclein-induced dopaminergic neurodegeneration by overexpression of the mitochondrial import receptor TOM20 in the rat midbrain
Authors: De Miranda Briana R. , Rocha Emily M. , Castro Sandra , Greenamyre J. Timothy
Published: May 2020

Dopaminergic neurons of the substantia nigra are selectively vulnerable to mitochondrial dysfunction, which is hypothesized to be an early and fundamental pathogenic mechanism in Parkinson’s disease (PD). Mitochondrial function depends on the successful import of nuclear-encoded proteins, many of which are transported through the TOM20-TOM22 outer mitochondrial membrane import receptor machinery. Recent data suggests that post-translational modifications ofα-synuclein promote its interaction with TOM20 at the outer mitochondrial membrane and thereby inhibit normal protein import, which leads to dysfunction and death of dopaminergic neurons. As such, preservation of mitochondrial import in the face of α-synuclein accumulation might be a strategy to prevent dopaminergic neurodegeneration, however, this is difficult to assess using currentin vivomodels of PD. To this end, we established an exogenous co-expression system, utilizing AAV2 vectors to overexpress human α-synuclein and TOM20, individually or together, in the adult Lewis rat substantia nigra in order to assess whether TOM20 overexpression attenuates α-synuclein-induced dopaminergic neurodegeneration. Twelve weeks after viral injection, we observed that AAV2-TOM20 expression was sufficient to prevent loss of nigral dopaminergic neurons caused by AAV2-αSyn overexpression. The observed TOM20-mediated dopaminergic neuron preservation appeared to be due, in part, to the rescued import of nuclear-encoded mitochondrial electron transport chain proteins that were inhibited by α-synuclein overexpression. In addition, TOM20 overexpression rescued the import of the chaperone protein GRP75/mtHSP70/mortalin, a stress-response protein involved in α-synuclein-induced injury. Collectively, these data indicate that TOM20 expression prevents α-synuclein-induced mitochondrial dysfunction, which is sufficient to rescue dopaminergic neurons in the adult rat brain.
The kinetic landscape of an RNA binding protein in cells
Authors: Sharma Deepak , Zagore Leah L. , Brister Matthew M. , Ye Xuan , Crespo-Hernández Carlos E. , Licatalosi Donny D. , Jankowsky Eckhard
Published: May 2020

Gene expression in higher eukaryotic cells orchestrates interactions between thousands of RNA binding proteins (RBPs) and tens of thousands of RNAs1. The kinetics by which RBPs bind to and dissociate from their RNA sites are critical for the coordination of cellular RNA-protein interactions2. However, these kinetics were experimentally inaccessible in cells. Here we show that time-resolved RNA-protein crosslinking with a pulsed femtosecond UV laser, followed by immunoprecipitation and high throughput sequencing allows the determination of binding and dissociation kinetics of the RBP Dazl for thousands of individual RNA binding sites in cells. This kinetic crosslinking and immunoprecipitation (KIN-CLIP) approach reveals that Dazl resides at individual binding sites only seconds or shorter, while the sites remain Dazl-free markedly longer. The data further indicate that Dazl binds to many RNAs in clusters of multiple proximal sites. The impact of Dazl on mRNA levels and ribosome association correlates with the cumulative probability of Dazl binding in these clusters. Integrating kinetic data with mRNA features quantitatively connects Dazl-RNA binding to Dazl function. Our results show how previously inaccessible, kinetic parameters for RNA-protein interactions in cells can be measured and how these data quantitatively link RBP-RNA binding to cellular RBP function.
Anti-GPR56 monoclonal antibody potentiates GPR56-mediated Src-Fak signaling to modulate cell adhesion
Authors: Chatterjee Treena , Zhang Sheng , Posey Tressie A. , Wu Ling , Yu Wangsheng , Liu Qingyun J. , Carmon Kendra S.
Published: May 2020

GPR56, also known as ADGRG1, is a member of the adhesion G protein-coupled receptor (aGPCR) family shown to play important roles in cell adhesion, brain development, immune system function, and tumorigenesis. GPR56 is upregulated in colorectal cancer and high expression correlates with poor prognosis. Several studies have shown that GPR56 couples to the Gα12/13class of heterotrimeric G-proteins to promote RhoA activation. However, due to its structural complexity and lack of a high affinity receptor-specific ligand, the complete GPR56 signaling mechanism still remains largely unknown. To delineate the activation mechanism and intracellular signaling functions of GPR56, we generated a monoclonal antibody (mAb) which binds GPR56 with high affinity and specificity to the extracellular domain (ECD). We show that overexpression of GPR56 in 293T cells lead to increased phosphorylation of Src, Fak, and paxillin adhesion proteins and activation of the Gα12/13-RhoA-mediated serum response factor (SRF) pathway. Treatment of cells with anti-GPR56 mAb potentiated Src-Fak phosphorylation, RhoA-SRF signaling, and cell adhesion. Consistently, knockdown of GPR56 in colorectal cancer cells decreased Src-Fak pathway phosphorylation and cell adhesion. Interestingly, GPR56-mediated activation of Src-Fak phosphorylation occurred independent of RhoA, yet mAb-induced potentiation of RhoA-SRF signaling was Src-dependent. Furthermore, we show that the Serine–Threonine–Proline-rich (STP) region of the ECD of GPR56 was not essential for mAb binding, yet was required for activation of Src-Fak signaling. These data support a new ECD-dependent mechanism by which GPR56 functions to regulate cell adhesion through activation of Src-Fak signaling.
Conspecific negative density dependence and why its study should not be abandoned
Authors: LaManna Joseph A. , Mangan Scott A. , Myers Jonathan A.
Published: May 2020

Recent studies showing bias in the measurement of density dependence have the potential to sow confusion in the field of ecology. We provide clarity by elucidating key conceptual and statistical errors with the null-model approach used in Detto et al. (2019). We show that neither their null model nor a more biologically-appropriate null model reproduces differences in density-dependent recruitment between forests, indicating that the latitudinal gradient in negative density dependence is not an artefact of statistical bias. Finally, we suggest a path forward that combines observational comparisons of density dependence in multiple fitness components across localities with mechanistic and geographically-replicated experiments.
Phage-DMS: a comprehensive method for fine mapping of antibody epitopes
Authors: Garrett Meghan E. , Itell Hannah L. , Crawford Katharine H.D. , Basom Ryan , Bloom Jesse D. , Overbaugh Julie
Published: May 2020

Understanding the antibody response is critical to developing vaccine and antibody-based therapies and has inspired the recent development of new methods to isolate antibodies. However, methods to define the antibody-antigen interactions that determine specificity or allow escape have not kept pace. We developed Phage-DMS, a method which combines two powerful approaches – immunoprecipitation of phage peptide libraries and deep mutational scanning (DMS) – to enable high-throughput fine mapping of antibody epitopes. As an example, we designed sequences encoding all possible amino acid variants of HIV Envelope to create phage display libraries. Using Phage-DMS, we identified sites of escape predicted using other approaches for four well characterized HIV monoclonal antibodies with known linear epitopes. In some cases, the results of Phage-DMS refined the epitope beyond what was determined in previous studies. This method has the potential to rapidly and comprehensively screen many antibodies in a single experiment to define sites essential for binding to antigen.
Spatial inhibition of return is impaired in mild cognitive impairment and mild Alzheimer’s disease
Authors: Jiang Xiong , Howard James H. , Rebeck G. Wiliam , Turner R. Scott
Published: May 2020

Spatial inhibition of return (IOR) refers to the phenomenon by which individuals are slower to respond to stimuli appearing at a previously cued location compared to un-cued locations. Here we provide evidence supporting that spatial IOR is mildly impaired in individuals with mild cognitive impairment (MCI) or mild Alzheimer’s disease (AD), and the impairment is readily detectable using a novel double cue paradigm. Furthermore, reduced spatial IOR in high-risk healthy older individuals is associated with reduced memory and other neurocognitive task performance, suggesting that the novel double cue spatial IOR paradigm may be useful in detecting MCI and early AD.

SIGNIFICANCE STATEMENT

Novel double cue spatial inhibition of return (IOR) paradigm revealed a robust effect IOR deficits in individuals with mild cognitive impairment (MCI) or mild Alzheimer’s disease (AD)

Spatial IOR effect correlates with memory performance in healthy older adults at a elevated risk of Alzheimer’s disease (with a family history or APOE e4 allele)

The data suggests that double cue spatial IOR may be sensitive to detect early AD pathological changes, which may be linked to disease progress at the posterior brain regions (rather than the medial temporal lobe)
Neurokinin 1 receptor activation in the rat spinal cord maintains latent sensitization, a model of inflammatory and neuropathic chronic pain
Authors: Chen Wenling , Marvizon Juan Carlos
Published: May 2020

Latent sensitization is a model of chronic pain in which a persistent state of pain hypersensitivity is suppressed by opioid receptors, as evidenced by the ability of opioid antagonists to induce a period of mechanical allodynia. Our objective was to determine if substance P and its neurokinin 1 receptor (NK1R) mediate the maintenance of latent sensitization. Latent sensitization was induced by injecting rats in the hindpaw with complete Freund’s adjuvant (CFA), or by spared nerve injury (SNI). When responses to von Frey filaments returned to baseline (day 28), the rats were injected intrathecally with saline or the NK1R antagonist RP67580, followed 15 min later by intrathecal naltrexone. In both pain models, the saline-injected rats developed allodynia for 2 h after naltrexone, but not the RP67580-injected rats. Saline or RP67580 were injected daily for two more days. Five days later (day 35), naltrexone was injected intrathecally. Again, the saline-injected rats, but not the RP67580-injected rats, developed allodynia in response to naltrexone. To determine if there is sustained activation of NK1Rs during latent sensitization, NK1R internalization was measured in lamina I neurons in rats injected in the paw with saline or CFA, and then injected intrathecally with saline or naltrexone on day 28. The rats injected with CFA had a small amount of NK1R internalization that was significantly higher than in the saline-injected rats. Naltrexone increased NK1R internalization in the CFA-injected rats but nor in the saline-injected rats. Therefore, sustained activation of NK1Rs maintains pain hypersensitivity during latent sensitization.
Exotic Hobos: Release, escape, and potential secondary dispersal of African red-headed agamas (Agama picticaudaPETERS, 1877) through the Florida railway systems
Authors: Gray Russell J.
Published: May 2020

Context

Invasive reptile species are introduced and established through a variety of distribution channels (e.g. accidental/intentional release by pet owners, hitchhiking on imported goods), and can be detrimental to native ecosystems. Understanding the origins and spread of non-native species can help land managers to make informed decisions when attempting to prevent future introductions and remove established populations.

Aims

The objectives of this study were to employ modelling techniques with open-source observational data to confirm putative local origins of African red-headed agamas in Florida and to locate potential distribution channels in which they are spreading throughout the state.

Methods

Geographic profiling, a technique commonly used for criminal investigations, was used along with suspected origin locations of introduced African red-headed agamas (Agama picticauda) from the literature and observations from the Early Detection and Distribution Mapping System (EDDMapS). Anchor points and their immediate surroundings were investigated for potential patterns of origination and dispersal.

Key results

The results of this study provide evidence that African red-headed agamas likely established themselves through both intentional releases and unintentional escapes from the pet owners and breeders, while also potentially hitchhiking on plant exports, and dispersing throughout Florida via the railway systems.

Conclusions

Given the potential for railways as a method of assisted dispersal, and given the potential exports they may be hitchhiking on, the results of this study suggest that railcars and railway export facilities should be included in future management of non-native African red-headed agamas in Florida.

Implications

The implications of this study builds on prior evidence that geographic profiling is an effective modelling tool in regards to biological invasions, which can accurately confirm suspected origins while also effectively mapping previously unknown epicenters of population clusters to be investigated by managers.
Individual Resting-state alpha peak frequency and within-trial changes in alpha peak frequency both predict visual flash segregation performance
Authors: Drewes Jan , Muschter Evelyn , Zhu Weina , Melcher David
Published: May 2020

Although sensory input is continuous, information must be combined over time to guide action and cognition, leading to the proposal of temporal sampling windows. A number of studies have suggested that a 10Hz sampling window might be involved in the “frame rate” of visual processing. To investigate this, we tested the ability of participants to localize and enumerate 1 or 2 visual flashes presented either at near-threshold (NT) or full contrast intensities, while recording magnetoencephalography (MEG). Performance was linked to the alpha frequency both at the individual level and trial-by-trial. Participants with a higher resting state alpha peak frequency showed the greatest improvement in performance as a function of ISI within the 100ms time window, while those with slower alpha improved more when ISI exceeded 100ms. On each trial, correct enumeration (1 vs. 2) performance was paired with faster pre-stimulus instantaneous alpha frequency. The effect of the timing of the NT stimulus on the perception was consistent with visual temporal integration windows being embedded in a sampling rhythm. Our results suggest that visual sampling/processing speed, linked to peak alpha frequency, is both an individual trait and varies in a state-dependent manner.

Significance Statement

A fundamental question in sensory and cognitive neuroscience is how the brain makes sense of the continuous flow of sensory input, parsing it into meaningful objects and events. The speed of cortical alpha rhythms is hypothesized to predict the temporal resolution of visual perception. We present a magnetoencephalography study investigating whether this temporal resolution is an individual trait or, in contrast, depends on fluctuations in brain state. Our results show that both individual resting state alpha frequency, a relatively stable trait, and trial-by-trial fluctuations of the instantaneous alpha frequency determine temporal segregation performance. These results have important implications for how our moment-by-moment perceptual experience is shaped as well as future intervention strategies to improve visual processing for specific tasks.
CTLA-4 blockade reverses the Foxp3+ T-regulatory-cell suppression of anti-tuberculosis T-cell effector responses
Authors: Shao Lingyun , Gao Yan , Shao Xiaoyi , Ou Qingfang , Zhang Shu , Liu Qianqian , Zhang Bingyan , Wu Jing , Ruan Qiaoling , Shen Ling , Weng Xinhua , Zhang Wenhong , Chen Zheng W.
Published: May 2020

Backgrounds

It has been well described that Foxp3+ T regulatory (Treg) cells suppress immune responses and that murine cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) can control the function of Foxp3+Treg cells. However, it remains unknown about the role of CTLA-4 pathway in Treg suppression of T cell responses in tuberculosis (TB).

Methods

We assessed TB-driven changes in CTLA-4-expressing Foxp3+ Treg and conducted CTLA-4 blocking mechanistic studies ex vivo in 126 subjects with active TB, latent TB or uninfected statuses.

Results

Frequencies of CTLA-4-expressing Treg cells were increased in the circulation of pulmonary TB patients and in the pleural compartment of TB pleuritis. Six-month anti-TB treatment significantly reduced CTLA-4+ Treg subset. Notably, antibody blocking of CTLA-4 pathway (CTLA-4 blockade) reversed the ability of Treg cells to suppress anti-TB Th1 responses and abrogated the Treg-mediated suppression of TB antigen-stimulated proliferative response. The CTLA-4 blockade reversed the Treg suppression of the ability of T cells to restrict intracellular BCG andM. tuberculosisgrowth in macrophages.

Interpretation

The study uncovered previously-unreported observations implicating that the CTLA-4 blockade abrogates the capability of Treg cells to suppress anti-TB immune responses or immunity. Findings support the rationale for exploring the CTLA-4 blockade as potential host-directed therapy against TB.

Fund

This work is supported in part by the National Natural Science Foundation of China (30901277, 81671553, 81501359), and the Key Technologies Research and Development Program for Infectious Diseases of China (2017ZX10201302-004).
Infection Groups Differential (IGD) Score Reveals Infection Ability Difference between SARS-CoV-2 and Other Coronaviruses
Authors: Song Ziwei , Zhou Xingchen , Cai Yuanyuan , Feng Shuo , Zhang Tingting , Wang Yun , Lai Maode , Li Jing
Published: May 2020

The Corona Virus Disease 2019 (COVID-19) pandemic that began in late December 2019 has resulted in millions of cases diagnosed worldwide. Reports have shown that SARS-CoV-2 shows extremely higher infection rates than other coronaviruses. This study conducted a phylogenetics analysis of 91 representative coronaviruses and found that the functional spike protein of SARS-CoV-2, which interacts with the human receptor ACE2, is actually not undergoing distinct selection pressure compared to other coronaviruses. Furthermore, we define a new measurement, infection group differential (IGD) score, in assessing the infection ability of two human coronavirus groups. There are nine extremely high IGD (ehIGD) sites in the receptor-binding domain (RBD) out of 40 high IGD (hIGD) sites that exhibit a unique infection-related pattern from the haplotype network and docking energy comparison. These 40 hIGD sites are basically conserved among the SARS-CoV-2, i.e. there are only two hIGD sites mutated in four out of 1,058 samples, defined as rare-mutation hIGD (rhIGD) sites. In conclusion, ehIGD and rhIGD sites might be of great significance to the development of vaccines.
TCF7L2Silencing Reprograms the 4D Nucleome of Colorectal Cancer Cells
Authors: Brown Markus A. , Dotson Gabrielle A. , Ronquist Scott , Emons Georg , Rajapakse Indika , Ried Thomas
Published: May 2020

Canonical Wnt signaling is crucial for intestinal homeostasis as the major Wnt signaling effector in the intestines, TCF4, is required for stem cell maintenance. The capability of TCF4 to maintain the stem cell phenotype is contingent upon β-catenin, a potent transcriptional activator which interacts with histone acetyltransferases and chromatin remodeling complexes. In colorectal cancer, mutations result in high levels of nuclear β-catenin causing aberrant cell growth. Here, we used RNAi to explore the influence of TCF4 on chromatin structure (Hi-C) and gene expression (RNA sequencing) across a 72-hour time series in colorectal cancer. We found that TCF4 reduction results in a disproportionate upregulation of gene expression genome-wide, including a powerful induction ofSOX2. Hi-C analysis revealed a general increase in chromatin compaction across the entire time series, though this did not influence gene expression. Analysis of local chromosome organization demonstrated a TAD boundary loss which influenced the expression of a cluster ofCEACAMgenes on chromosome 19. Four-dimensional nucleome (4DN) analysis, which integrates structural (Hi-C) and functional (RNA sequencing) data, identified EMT and E2F as the two most deregulated pathways andLUM, TMPO, andAURKAas highly influential genes in these networks. Results from gene expression, chromatin structure, and centrality analyses were then integrated to generate a list of candidate transcription factors for reprogramming of colorectal cancer cells to a vulnerable state. The top ranked transcription factor in our analysis was c-JUN, an oncoprotein known to interact with TCF4 and β-catenin.
Kinetics of Atg2-mediated lipid transfer from the ER can account for phagophore expansion
Authors: von Bülow Sören , Hummer Gerhard
Published: May 2020

The protein Atg2 has been proposed to form a membrane tether that mediates lipid transfer from the ER to the phagophore in autophagy. However, recent kinetic measurements on the human homolog ATG2A indicated a transport rate of only about one lipid per minute, which would be far too slow to deliver the millions of lipids required to form a phagophore on a physiological time scale. Here, we revisit the analysis of the fluorescence quenching experiments. We develop a detailed kinetic model of the lipid transfer between two membranes bridged by a tether that forms a conduit for lipids. The model provides an excellent fit to the fluorescence experiments, with a lipid transfer rate of about 100 per second and protein. At this rate, Atg2-mediated transfer can supply a significant fraction of the lipids required in autophagosome biogenesis. Our kinetic model is generally applicable to lipid-transfer experiments, in particular to proteins forming organelle contact sites in cells.
Rescuing AAV gene transfer from antibody neutralization with an IgG-degrading enzyme
Authors: Elmore Zachary C. , Oh Daniel K. , Simon Katherine E. , Fanous Marcos M. , Asokan Aravind
Published: May 2020

Pre-existing humoral immunity to recombinant adeno-associated viral (AAV) vectors restricts the treatable patient population and efficacy of human gene therapies. Approaches to clear neutralizing antibodies (NAbs), such as plasmapheresis and immunosuppression are either ineffective or cause undesirable side effects. Here, we describe a clinically relevant strategy to rapidly and transiently degrade NAbs prior to AAV administration using an IgG degrading enzyme (IdeZ). We demonstrate that recombinant IdeZ efficiently cleaves IgG in dog, monkey and human antisera. Prophylactically administered IdeZ cleaves circulating, human IgG in mice and prevents AAV neutralizationin vivo. In macaques, a single intravenous dose of IdeZ rescues AAV transduction by transiently reversing seropositivity. Importantly, IdeZ efficiently cleaves NAbs and rescues AAV transduction in mice passively immunized with individual human donor sera representing a diverse population. Our antibody clearance approach presents a new paradigm for expanding the prospective patient cohort and improving efficacy of AAV gene therapy.
Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens
Authors: Hogan Catherine A. , Garamani Natasha , Lee Andrew S. , Tung Jack K. , Sahoo Malaya K. , Huang ChunHong , Stevens Bryan , Zehnder James , Pinsky Benjamin A.
Published: May 2020

Background

Several point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for diagnosis of SARS-CoV-2. The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use.

Objectives

The aim of this study was to assess test performance of the Accula SARS-CoV-2 test.

Study design

The performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT) targeting the envelope (E) gene. Assay concordance was assessed by overall percent agreement, positive percent agreement (PPA), negative percent agreement (NPA), and Cohen’s kappa coefficient.

Results

Overall percent agreement between the assays was 84.0% (95% confidence interval [CI] 75.3 to 90.6%), PPA was 68.0% (95% CI 53.3 to 80.5%) and the kappa coefficient was 0.68 (95% CI 0.54 to 0.82). Sixteen specimens detected by the SHC-LDT were not detected by the Accula test, and showed low viral load burden with a median cycle threshold value of 37.7. NPA was 100% (95% CI 94.2 to 100%).

Conclusion

Compared to the SHC-LDT, the Accula SARS-CoV-2 test showed excellent negative agreement. However, positive agreement was low for samples with low viral load. The false negative rate of the Accula POC test calls for a more thorough evaluation of POC test performance characteristics in clinical settings, and for confirmatory testing in individuals with moderate to high pre-test probability of SARS-CoV-2 who test negative on Accula.
Sensitivity to food and cocaine cues are independent traits in a large sample of heterogeneous stock rats
Authors: King Christopher P. , Tripi Jordan A. , Hughson Alesa R. , Horvath Aidan P. , Lamparelli Alexander C. , Holl Katie L. , Chitre Apurva , Polesskaya Oksana , Richards Jerry B. , Woods Leah C. Solberg , Palmer Abraham A. , Robinson Terry E. , Flagel Shelly B. , Meyer Paul J.
Published: May 2020

Sensitivity to cocaine and its associated stimuli (“cues”) are important factors in the development and maintenance of addiction. Rodent studies suggest that this sensitivity is related, in part, to the propensity to attribute incentive salience to food cues, which, in turn, contributes to the maintenance of cocaine self-administration, and cue-induced relapse of drug-seeking. Whereas each of these traits has established links to drug use, the relatedness between the individual traits themselves has not been well characterized in preclinical models. To this end, the propensity to attribute incentive salience to a food cue was first assessed in a large population of 2716 outbred heterogeneous stock rats. We then determined whether this was associated with performance in two paradigms (cocaine conditioned cue preference and cocaine contextual conditioning). These measure the unconditioned locomotor effects of cocaine, as well as conditioned approach and the locomotor response to a cocaine-paired floor or context. There was large individual variability and sex differences among all traits, but they were largely independent of one another in both males and females. These findings suggest that these traits may contribute to drug-use via independent underlying neuropsychological processes.
Farm yard manure enhances phosphate fertilizer use efficiency in different upland rice genotypes through mitigating aluminium toxicity
Authors: De Bauw Pieterjan , Shimamura Erina , Rakotoson Tovohery , Andriamananjara Andry , Verbeeck Mieke , Merckx Roel , Smolders Erik
Published: May 2020

Upland rice production on weathered soils is often constrained by phosphorus (P) deficiency and soil acidity. Farmyard manure application (FYM) can sharply enhance yields and agronomic P fertilizer (TSP) efficiency. We tested the hypothesis that rice genotypes differ in the extent of using organic P and offering distinct benefits under TSP-FYM combinations. Multiple field trials were conducted in the uplands of Madagascar, with factorial combinations of six genotypes, FYM, and TSP applications, with blanket N&K additions. Rice grain yields reached 6 t ha-1after three years of TSP+FYM application, were lower when FYM or TSP were used separately, while crops failed under zero P input. Genotypic differences were inferior to the large treatment effects. Application of FYM increased soil pH and CaCl2-extractable P while decreasing CaCl2-extractable aluminium. An additional liming trial indicated that beneficial effects of FYM over TSP relate to liming effects. Genotypic ranking of yields and agronomic efficiency was inconsistent, without superior genotypes under FYM versus TSP. However, Chomrong Dhan and FOFIFA 172 showed superior yields under TSP+FYM. The FYM application lowers aluminium toxicity which overrules potential effects of organic P supply. Aluminium tolerance should be included when developing rice genotypes for low P tolerance in weathered soils.
Small interfering RNAs are highly effective inhibitors regarding Crimean-Congo hemorrhagic fever virus replicationin vitro
Authors: Földes Fanni , Madai Mónika , Papp Henrietta , Kemenesi Gábor , Zana Brigitta , Geiger Lili , Gombos Katalin , Somogyi Balázs , Bock-Marquette Ildikó , Jakab Ferenc
Published: May 2020

Crimean-Congo hemorrhagic fever virus (CCHFV) is one of the prioritized diseases of World Health Organization, considering its potential to create a public health emergency and more importantly, the absence of efficacious drugs and/or vaccines regarding treatment. The highly lethal nature characteristic to CCHFV restricts research to BSL-4 laboratories, which complicates effective research and developmental strategies. In consideration of antiviral therapies, RNA interference can be used to suppress viral replication by targeting viral genes. RNA interference uses small interfering RNAs (siRNAs) to silence genes. The aim of our study was to design siRNAs that inhibit CCHFV replication and can serve as a basis for further antiviral therapies. A549 cells were infected with CCHFV after transfection with the siRNAs. Following 72 hours, nucleic acid from the supernatant was extracted for Droplet Digital PCR analysis. Among the investigated siRNAs we identified four effective candidates against all three segments of CCHF genome: one for the S and M segments, whilst two for the L segment. Consequently, blocking any segment of CCHFV leads to changes in the virus copy number that indicates an antiviral effect of the siRNAsin vitro. The most active siRNAs were demonstrated a specific inhibitory effect against CCHFV in a dose-dependent manner. In summary, we demonstrated the ability of specific siRNAs to inhibit CCHFV replicationin vitro. This promising result can be used in future anti-CCHFV therapy developments.
Targeted mutation of barley (1,3;1,4)-β-glucan synthases reveals complex relationships between the storage and cell wall polysaccharide content
Authors: Garcia-Gimenez Guillermo , Barakate Abdellah , Smith Pauline , Stephens Jennifer , Khor Shi F. , Doblin Monika S. , Hao Pengfei , Bacic Antony , Fincher Geoffrey B. , Burton Rachel A. , Waugh Robbie , Tucker Matthew R. , Houston Kelly
Published: May 2020

Barley (Hordeum vulgareL) grain is comparatively rich in (1,3;1,4)-β-glucan, a source of fermentable dietary fibre that protects against various human health conditions. However, low grain (1,3;1,4)-β-glucan content is preferred for brewing and distilling. We took a reverse genetics approach, using CRISPR/Cas9 to generate mutations in members of theCellulose synthase-like(Csl) gene superfamily that encode known (HvCslF6andHvCslH1) and putative (HvCslF3andHvCslF9) (1,3;1,4)-β-glucan synthases. Resultant mutations ranged from single amino acid (aa) substitutions to frameshift mutations causing premature stop codons, and led to specific differences in grain morphology, composition and (1,3;1,4)-β-glucan content. (1,3;1,4)-β-Glucan was absent in the grain ofcslf6knock-out lines whereascslf9knock-out lines had similar (1,3;1,4)-β-glucan content to WT. However,cslf9mutants showed changes in the abundance of other cell wall-related monosaccharides compared to WT. Thousand grain weight (TGW), grain length, width and surface area were altered incslf6knock-outs and to a lesser extent TGW incslf9knock-outs. cslf3andcslh1mutants had no effect on grain (1,3;1,4)-β-glucan content. Our data indicate that multiple members of theCslF/Hfamily fulfil important functions during grain development but, with the exception ofHvCslF6, do not impact the abundance of (1,3;1,4)-β-glucan in mature grain.
Pervasive non-CpG methylation at zebrafish mosaic satellite repeats
Authors: Ross Samuel E , Angeloni Allegra , de Mendoza Alex , Bogdanovic Ozren
Published: May 2020

In vertebrates, DNA methylation predominantly occurs at CG dinucleotides even though widespread non-CG methylation (mCH) has been reported in mammalian embryonic and neural cells. Unlike in mammals, where mCH is found enriched at CAC/G trinucleotides and is tissue-restricted, we find that zebrafish embryos as well as adult somatic and germline tissues display robust methylation enrichment at TGCT positions associated with mosaic satellite repeats. These repeats reside in H3K9me3-marked heterochromatin and display mCH reprogramming coincident with zygotic genome activation. Altogether, this work provides insight into a novel form of vertebrate mCH and highlights the substrate diversity of vertebrate DNA methyltransferases.
Disease-relevant single cell photonic signatures identify S100β stem cells and their myogenic progeny in vascular lesions
Authors: Molony Claire , King Damien , Di Luca Mariana , Kitching Michael , Olayinka Abidemi , Hakimjavadi Roya , Julius Lourdes A.N. , Fitzpatrick Emma , Gusti Yusof , Burtenshaw Denise , Healy Killian , Finlay Emma K. , Kernan David , Llobera Andreu , Liu Weimin , Morrow David , Redmond Eileen M. , Ducrée Jens , Cahill Paul A.
Published: May 2020

A hallmark of subclinical atherosclerosis is the accumulation of vascular smooth muscle cell (SMC)-like cells leading to intimal thickening and lesion formation. While medial SMCs contribute to vascular lesions, the involvement of resident vascular stem cells (vSCs) remains unclear. We evaluated single cell photonics as a discriminator of cell phenotypein vitrobefore the presence of vSC within vascular lesions was assessedex vivousing supervised machine learning and further validated using lineage tracing analysis. Using a novel lab-on-a-Disk (Load) platform, label-free single cell photonic emissions from normal and injured vesselsex vivowere interrogated and compared to freshly isolated aortic SMCs, cultured Movas SMCs, macrophages, B-cells, S100β+mVSc, bone marrow derived mesenchymal stem cells (MSC) and their respective myogenic progeny across five broadband light wavelengths (λ465 – λ670 ± 20 nm). We found that profiles were of sufficient coverage, specificity, and quality to clearly distinguish medial SMCs from different vascular beds (carotid vs aorta), discriminate normal carotid medial SMCs from lesional SMC-like cellsex vivofollowing flow restriction, and identify SMC differentiation of a series of multipotent stem cells following treatment with transforming growth factor beta 1 (TGF-β1), the Notch ligand Jaggedl, and Sonic Hedgehog using multivariate analysis, in part, due to photonic emissions from enhanced collagen III and elastin expression. Supervised machine learning supported genetic lineage tracing analysis of S100β+vSCs and identified the presence of S100β+vSC-derived myogenic progeny within vascular lesions. We conclude disease-relevant photonic signatures may have predictive value for vascular disease.