bluuebunny/crossref_metadata_2025 huggingface dataset:
In vitro inactivation of SARS-CoV-2 with 0.5% povidone iodine nasal spray (Nasodine) at clinically relevant concentrations and timeframes using tissue culture and PCR based assays
Authors: Tucker S.P. , Goodall S. , Julander J. , Mendenhall M. , Friedland P. , Molloy P.L.
Published: February 2021

BACKGROUND

There has been considerable speculation regarding the potential of PVP-I nasal disinfection as an adjunct to other countermeasures during the ongoing SARS-CoV-2 pandemic. Nasodine is a commercial formulation of 0.5% PVP-I that has been evaluated for safety and efficacy in human trials as a treatment for the common cold, including a Phase III trial (ANZCTR: ACTRN12619000764134). This study presents the first report of thein vitroefficacy of this formulation against SARS-CoV-2.

METHODS

We conductedin vitroexperiments to determine if the PVP-I formulation inactivated SARS-CoV-2 using two independent assays and virus isolates, and incorporating both PCR-based detection and cell culture methods to assess residual virus after exposure to the formulation.

RESULTS

Based on cell culture results, the PVP-I formulation was found to rapidly inactivate SARS-CoV-2 isolatesin vitroin short timeframes (15 seconds to 15 minutes) consistent with the minimum and maximum potential residence time in the nose. The Nasodine formula was found to be more effective than 0.5% PVP-I in saline. Importantly, it was found that the formulation inactivated culturable virus but had no effect on PCR-detectable viral RNA.

CONCLUSIONS

The PVP-I formulation eliminated the viability of SARS-CoV-2 virus with short exposure times consistent with nasal use. PCR alone may not be adequate for viral quantification in nasal PVP-I studies; future studies should incorporate cell culture to assess viral viability. Nasal disinfection with PVP-I may be a useful intervention for newly-diagnosed COVID-19 patients to reduce transmission risk and disease progression to the lower respiratory tract.
Evolution of the bread wheat D-subgenome and enriching it with diversity fromAegilops tauschii
Authors: Gaurav Kumar , Arora Sanu , Silva Paula , Sánchez-Martín Javier , Horsnell Richard , Gao Liangliang , Brar Gurcharn S. , Widrig Victoria , Raupp Jon , Singh Narinder , Wu Shuangye , Kale Sandip M. , Chinoy Catherine , Nicholson Paul , Quiroz-Chávez Jesús , Simmonds James , Hayta Sadiye , Smedley Mark A. , Harwood Wendy , Pearce Suzi , Gilbert David , Kangara Ngonidzashe , Gardener Catherine , Forner-Martínez Macarena , Liu Jiaqian , Yu Guotai , Boden Scott , Pascucci Attilio , Ghosh Sreya , Hafeez Amber N. , O’Hara Tom , Waites Joshua , Cheema Jitender , Steuernagel Burkhard , Patpour Mehran , Justesen Annemarie Fejer , Liu Shuyu , Rudd Jackie C. , Avni Raz , Sharon Amir , Steiner Barbara , Kirana Rizky Pasthika , Buerstmayr Hermann , Mehrabi Ali A. , Nasyrova Firuza Y. , Chayut Noam , Matny Oadi , Steffenson Brian J. , Sandhu Nitika , Chhuneja Parveen , Lagudah Evans , Elkot Ahmed F. , Tyrrell Simon , Bian Xingdong , Davey Robert P. , Simonsen Martin , Schauser Leif , Tiwari Vijay K. , Kutcher H. Randy , Hucl Pierre , Li Aili , Liu Deng-Cai , Mao Long , Xu Steven , Brown-Guedira Gina , Faris Justin , Dvorak Jan , Luo Ming-Cheng , Krasileva Ksenia , Lux Thomas , Artmeier Susanne , Mayer Klaus F. X. , Uauy Cristobal , Mascher Martin , Bentley Alison R. , Keller Beat , Poland Jesse , Wulff Brande B. H.
Published: February 2021

Aegilops tauschii,the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. To better define and understand this diversity, we sequenced 242Ae. tauschiiaccessions and compared them to the wheat D-subgenome. We characterized a rare, geographically-restricted lineage ofAe. tauschiiand discovered that it contributed to the wheat D-subgenome, thereby elucidating the origin of bread wheat from at least two independent hybridizations. We then usedk-mer-based association mapping to identify discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of ‘synthetic’ hexaploids incorporating diverseAe. tauschiigenomes. This pipeline permits rapid trait discovery in the diploid ancestor through to functional genetic validation in a hexaploid background amenable to breeding.
Regulation of lateral root development by shoot-sensed far-red light via HY5 is nitrate-dependent and involves the NRT2.1 nitrate transporter
Authors: van Gelderen Kasper , Kang Chiakai , Li Peijin , Pierik Ronald
Published: February 2021

Plants are very effective in responding to environmental changes during competition for light and nutrients. Low Red:Far-Red (low R:FR)-mediated neighbor detection allows plants to compete successfully with other plants for available light. This above-ground signal can also reduce lateral root growth by inhibiting lateral root emergence, a process that might help the plant invest resources in shoot growth. Nitrate is an essential nutrient for plant growth andArabidopsis thalianaresponds to low nitrate conditions by enhancing nutrient uptake and reducing lateral and main root growth. There are indications that low R:FR signaling and low nitrate signaling can affect each other. It is unknown which response is prioritized when low R:FR light- and low nitrate signaling co-occur. We investigated the effect of low nitrate conditions on the low R:FR response of theA. thalianaroot system in agar plate media, combined with the application of supplemental Far-Red (FR) light to the shoot. We observed that under low nitrate conditions main and lateral root growth was reduced, but more importantly, that the response of the root system to low R:FR was suppressed. Consistently, a loss-of-function mutant of a nitrate transporter geneNRT2.1lacked low R:FR-induced lateral root reduction and its root growth was hypersensitive to low nitrate. ELONGATED HYPOCOTYL5 (HY5) plays an important role in the root response to low R:FR and we found that it was less sensitive to low nitrate conditions with regards to lateral root growth. In addition, we found that low R:FR increasesNRT2.1expression and that low nitrate enhancesHY5expression. HY5 also affectsNRT2.1expression, however, it depended on the presence of ammonium in which direction this effect was. Replacing part of the nitrogen source with ammonium also removed the effect of low R:FR on the root system, showing that changes in nitrogen sources can be crucial for root plasticity. Together our results show that nitrate signaling can repress low R:FR responses and that this involves signaling via HY5 and NRT2.1.
Monitoring mitochondrial translation by pulse SILAC
Authors: Imami Koshi , Selbach Matthias , Ishihama Yasushi
Published: February 2021

Mitochondrial ribosomes are specialized to translate the 13 membrane proteins encoded in the mitochondrial genome, which shapes the oxidative phosphorylation (OXPHOS) complexes essential for cellular energy metabolism. Despite the importance of mitochondrial translation control, it is challenging to identify and quantify the mitochondrial-encoded proteins due to their hydrophobic nature and low abundance. Here, we introduce a mass spectrometry-based proteomic method that combines biochemical isolation of mitochondria with pulse stable isotope labeling by amino acids in cell culture (pSILAC). Our method provides the highest protein identification rate with the shortest measurement time among currently available methods, enabling us to quantify 12 out of the 13 mitochondrial-encoded proteins. We applied this method to uncover the global picture of (post-)translational regulation of both mitochondrial- and nuclear-encoded subunits of OXPHOS complexes. We found that inhibition of mitochondrial translation led to degradation of orphan nuclear-encoded subunits that are considered to form subcomplexes with the mitochondrial-encoded subunits. The results also allowed us to infer the subcomplex members of each OXPHOS complex. This method should be readily applicable to study mitochondrial translation programs in many contexts, including oxidative stress and mitochondrial disease.
Identification of anti-severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) oxysterol derivatives in vitro
Authors: Ohashi Hirofumi , Wang Feng , Stappenbeck Frank , Tsuchimoto Kana , Kobayashi Chisa , Saso Wakana , Kataoka Michiyo , Kuramochi Kouji , Muramatsu Masamichi , Suzuki Tadaki , Sureau Camille , Takeda Makoto , Wakita Takaji , Parhami Farhad , Watashi Koichi
Published: February 2021

Development of effective antiviral drugs targeting the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) are urgently needed to combat the coronavirus disease 2019 (COVID-19). Oxysterols, defined as oxidized derivatives of cholesterol, include endogenous (naturally occurring) cholesterol metabolites as well as semi-synthetic oxysterol derivatives. We have previously studied the use of semi-synthetic oxysterol derivatives as drug candidates for inhibition of cancer, fibrosis, and bone regeneration. In this study, we have screened a panel of naturally occurring and semi-synthetic oxysterol derivatives for anti-SARS-CoV-2 activity, using a cell culture infection assay. We show that the natural oxysterols, 7-ketocholesterol, 22(R)-hydroxycholesterol, 24(S)-hydroxycholesterol, and 27-hydroxycholesterol, substantially inhibited SARS-CoV-2 propagation in cultured cells. Among semi-synthetic oxysterols, Oxy186 displayed antiviral activity comparable to natural oxysterols. In addition, related oxysterol analogues Oxy210 and Oxy232 displayed more robust anti-SARS-CoV-2 activities, reducing viral replication more than 90% at 10 μM and 99% at 15 μM, respectively. When orally administered in mice, peak plasma concentrations of Oxy210 fall into a therapeutically relevant range (19 μM), based on the dose-dependent curve for antiviral activity in our cell culture infection assay. Mechanistic studies suggest that Oxy210 reduced replication of SARS-CoV-2 with disrupting the formation of double membrane vesicles (DMVs), intracellular membrane compartments associated with viral replication. Oxy210 also inhibited the replication of hepatitis C virus, another RNA virus whose replication is associated with DMVs, but not the replication of the DMV-independent hepatitis D virus. Our study warrants further evaluation of Oxy210 and Oxy232 as a safe and reliable oral medication, which could help protect vulnerable populations with increased risk developing COVID-19.
The secreted peptide IRP functions as a DAMP in rice immunity
Authors: Wang Pingyu , Jia Huimin , Guo Ting , Zhang Yuanyuan , Li Zhengguo , Kawano Yoji
Published: February 2021

Small signaling peptides play important roles in various plant processes, but information regarding their involvement in plant immunity is limited. We previously identified a novel small secreted protein in rice, named immune response peptide (IRP) by the integrated multi-omics analyses. Here, we studied IRP functions in rice immunity. Rice plants overexpressingIRPenhanced resistance to the blast fungus. Application of the IRP peptide to rice suspension cells triggered the expression ofIRPitself and defense genePAL1. RNA-seq results revealed that 84% of genes upregulated by IRP peptide were also induced by chitin, including 13OsWRKYtranscription factors, indicating that IRP and chitin share the similar signaling pathway. Co-treatment with chitin and IRP elevated the expression level ofPAL1andOsWRKYs in an additive manner. When results ofIRPandPAL1expression and MAPK activation by IRP were compared with those by chitin, IRP had a stronger effect on MAPK activation rather thanIRPandPAL1expression. Collectively, our findings indicate that IRP functions as a damage-associated molecular pattern (DAMP) in rice immunity, regulating MAPKs andOsWRKYs to amplify chitin signaling, and provide new insights into how PAMPs and DAMPs cooperatively regulate rice immunity.
Non-essential ribosomal proteins in bacteria and archaea identified using COGs
Authors: Galperin Michael Y. , Wolf Yuri I. , Garushyants Sofya K. , Alvarez Roberto Vera , Koonin Eugene V.
Published: February 2021

Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from the one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.

IMPORTANCE

In many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 21 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential inEscherichia coliandBacillus subtilis. These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.
Half-life of biodegradable plastics in the marine environment depends on material, habitat, and climate zone
Authors: Lott Christian , Eich Andreas , Makarow Dorothée , Unger Boris , Eekert Miriam van , Schuman Els , Reinach Marco Segre , Lasut Markus T. , Weber Miriam
Published: February 2021

The performance of the biodegradable plastic materials polyhydroxyalkanoate (PHA), polybutylene sebacate (PBSe) and polybutylene sebacate co-terephthalate (PBSeT), and of polyethylene (LDPE) was assessed under marine environmental conditions in a three-tier approach. Biodegradation lab tests (20 °C) were complemented by mesocosm tests (20 °C) with natural sand and seawater and by field tests in the warm-temperate Mediterranean Sea (12 – 30 °C) and in tropical Southeast Asia (29 °C) in three typical coastal scenarios. Plastic film samples were exposed in the eulittoral beach, the pelagic open water and the benthic seafloor and their disintegration monitored over time. We used statistical modelling to predict the half-life for each of the materials under the different environmental conditions to render the experimental results numerically comparable across all experimental conditions applied. The biodegradation performance of the materials differed by orders of magnitude depending on climate, habitat and material and revealed the inaccuracy to generically term a material ‘marine biodegradable’. The half-lifet0.5of a film of PHA with 85 μm thickness ranged from 54 d on the seafloor in SE Asia to 1247 d in mesocosm pelagic tests.t0.5for PBSe (25 μm) ranged from 99 d in benthic SE Asia to 2614 d in mesocosm benthic tests, and for PBSeTt0.5ranged from 147 d in the mesocosm eulittoral to 797 d in Mediterranean benthic field tests. For LDPE no biodegradation could be observed. These data can now be used to estimate the persistence of plastic objects should they end up in the marine environments considered here and will help to inform the life cycle (impact) assessment of plastics in the open environment.
DRDOCK: A Drug Repurposing platform integrating automated docking, simulations and a log-odds-based drug ranking scheme
Authors: Tsai Kun-Lin , Chang Sui-Yuan , Yang Lee-Wei
Published: February 2021

Motivation

Drug repurposing, where drugs originally approved to treat a disease are reused to treat other diseases, has received escalating attention especially in pandemic years. Structure-based drug design, integrating small molecular docking, molecular dynamic (MD) simulations and AI, has demonstrated its evidenced importance in streamlining new drug development as well as drug repurposing. To perform a sophisticated and fully automated drug screening using all the FDA drugs, intricate programming, accurate drug ranking methods and friendly user interface are very much needed.

Results

Here we introduce a new web server, DRDOCK,DrugRepurposingDOcking withConformation-sampling and pose re-ranKing - refined by MD and statistical models, which integrates small molecular docking and molecular dynamic (MD) simulations for automatic drug screening of 2016 FDA-approved drugs over a user-submitted single-chained target protein. The drugs are ranked by a novel drug-ranking scheme using log-odds (LOD) scores, derived from feature distributions of true binders and decoys. Users can submit a selection of LOD-ranked poses for further MD-based binding affinity evaluation. We demonstrated that our platform can indeed recover one of the substrates for nsp16, a cap ribose 2′-O methyltransferase, and recommends that fluralaner, tegaserod and fenoterol could be repurposed for the COVID19 treatment with the latter two being confirmed in SARS-CoV2 suppression experiments. All the sampled docking poses and trajectories can be 3D-viewed and played via our web interface. This platform shall be easy-to-use for general scientists and medicinal researchers to carry out drug repurposing within a couple of days which should add value to our timely responses to, particularly, emergent disease outbreaks.

Availability and implementation

DRDOCK can be freely accessed fromhttps://dyn.life.nthu.edu.tw/drdock/. (Due to the hardware upgrade, the service is NOT available before 7/18, 2021)
Learning and attention increase visual response selectivity through distinct mechanisms
Authors: Poort Jasper , Wilmes Katharina A. , Blot Antonin , Chadwick Angus , Sahani Maneesh , Clopath Claudia , Mrsic-Flogel Thomas D. , Hofer Sonja B. , Khan Adil G.
Published: February 2021

Selectivity of cortical neurons for sensory stimuli can increase across days as animals learn their behavioral relevance, and across seconds when animals switch attention. While both phenomena are expressed in the same cortical circuit, it is unknown whether they rely on similar mechanisms. We imaged activity of the same neuronal populations in primary visual cortex as mice learned a visual discrimination task and subsequently performed an attention switching task. Selectivity changes due to learning and attention were uncorrelated in individual neurons. Selectivity increases after learning mainly arose from selective suppression of responses to one of the task relevant stimuli but from selective enhancement and suppression during attention. Learning and attention differentially affected interactions between excitatory and PV, SOM and VIP inhibitory cell classes. Circuit modelling revealed that cell class-specific top-down inputs best explained attentional modulation, while the reorganization of local functional connectivity accounted for learning related changes. Thus, distinct mechanisms underlie increased discriminability of relevant sensory stimuli across longer and shorter time scales.
Hedgehog pathway inhibitors significantly reduce the formation of heterotopic ossification in a direct trauma/burn mouse model
Authors: Chakraborty Atanu , Gvozdenovic-Jeremic Jelena , Wang Fang , Hoag Stephen W. , Vert-Wong Ekaterina , Pearson Ryan M.
Published: February 2021

Heterotopic ossification (HO), either acquired or hereditary, is featured by ectopic bone formation outside of the normal skeleton. The acquired form of HO is a debilitating and common complication of musculoskeletal trauma, central nervous system injury, burns, combat trauma, hip and elbow fractures, and total joint replacement surgeries. It can be characterized as abnormal bone formation that occurs mostly by endochondral ossification. Recent studies have implicated inflammation and dysregulation of Hedgehog (Hh) signaling as major early contributors to HO formation. Here, we demonstrate that administration of the Hh pathway inhibitor, arsenic trioxide (ATO), prevented acquired HO in a clinically-relevant trauma/burn mouse model. We further evaluated the effects of two additional Hh pathway antagonists: cholecalciferol and pravastatin on mitigating osteoblast differentiation. Finally, we assessed the effect of a combination of Hh pathway inhibitors on reducing systemic proinflammatory responses. A targeted combination approach using Hh pathway inhibitors may offer potential therapeutic benefits though targeting differential components of the Hh pathway. Taken together, our study demonstrates that the administration of single or multiple Hh pathway inhibitors may have the potential to reduce the formation of acquired HO.
The Prognostic Value of Tumor-Infiltrating Immune Cells in Gynecologic Cancers
Authors: Chen Waichung , Hu Tuo , He Chunbo
Published: February 2021

Immunotherapy has changed the standard of treatment for many cancers. However, only a small number of gynecologic cancer patients benefit from immunotherapy. The intra-tumoral immune landscapes are suggested as a predictor of the response to immunotherapies, but there are no studies that provide a comprehensive immune characterization for gynecologic cancers. To characterize cellular compositions of the immune infiltrates and investigate if the immune landscape is a predictor for patient prognosis in gynecologic cancers, we analyzed tumor immune infiltrates of ovarian cancer, cervical cancer, and uterine cancer from The Cancer Genome Atlas Program (TCGA) using QuanTIseq and EPIC. Ovarian cancer had the highest percentage of total immune cells. Cervical cancer and uterine corpus endometrial carcinoma have lower percentages of immune cells with 17% and 16%, respectively. Furthermore, ovarian cancer had a significantly higher monocyte and M2-liked macrophage percentage, but a lower percentage for CD8 T cells and neutrophils compared to cervical cancer and uterine cancer. Cervical cancer had the highest percentage for M1-liked macrophages and the lowest for CD4 T cells. Uterine cancer had the highest percentage of dendritic cells. In cervical cancer, higher cell infiltration of CD8 T-Cells and M2-liked macrophages was associated with a better prognosis. In uterine cancer, patients with a higher number of dendritic cells and CD8 T-Cells had significantly better clinical outcomes. However, higher CD4 T-cell infiltration was associated with a poor prognosis in uterine cancer. Interestingly, the patient survival was not affected by the infiltration of any individual immune cells which we analyzed in ovarian cancer. We identified and validated four immune subtypes associated with distinct immune cell infiltration in gynecologic cancers. Cervical and uterine cancer patients from an immune-desert subtype that had the least amount of lymphocyte infiltration and a high level of monocyte had the worst prognosis. By contrast, cervical and uterine cancer patients from an immune-warm subtype that had higher infiltration of CD8 T-cell, natural killer (NK) cells, and dendritic cells (DCs) had the best prognosis. However, the survival rate of ovarian cancer patients is similar among the four different subtypes. Our study provides a conceptual framework to understand the tumor immune microenvironment of different gynecologic cancers.
Effect of Silicon Application on Leaf mineral Composition of Eucalyptus
Authors: Kumar Rahul , Reddy Dilip Kumar , Kaushik Prashant
Published: February 2021

Eucalyptus is a commonly planted tree in North India and its cultivation area is increasing. Leaves of Eucalyptus are used for tea which has healing properties and many other economic uses. Silicon is the second most abundant element in the earth’s crust next to oxygen. Silicon (Si) can improve photosynthesis, decrease transpiration, increase water use efficiency and provide resistance against biotic and abiotic stress. The clear information was not available regarding Silicon nourishment in tree species like Eucalyptus. Although a positive in plant development and overall dry matter production was noticed in Eucalyptus with Si application. The amount of nitrogen (N), phosphorus (P), and potassium (K) were inclined leaf whereas Calcium (Ca) and magnesium (Mg) content was not affected by Si application potassium silicate (K2SiO3). Finally results revealed that upon Si application significant increase in the leaf mineral content in almost all genotypes was recorded. Correlation studies revealed that leaf N and P were highly and significantly correlated with leaf copper (Cu) and iron (Fe) content, leaf Mg and leaf Cu were positively and significantly correlated with leaf N, manganese (Mn) and Fe content, leaf Mn and Fe content were highly and significantly correlated with leaf N, Mg and Cu content. To our detailed knowledge this is the first ever study conducted in Eucalyptus. Here the influence of potassium silicate on popular North Indian cultivars’ leaf mineral content Nevertheless, more studies are required to analyze the effect of Si application in tree species like Eucalyptus.
Outer Hair Cell Function is Normal in βV Spectrin Knockout Mice
Authors: Stankewich Michael C. , Bai Jun-Ping , Stabach Paul R. , Khan Saaim , Tan Winston J.T. , Surguchev Alexei , Song Lei , Morrow Jon S. , Santos-Sacchi Joseph , Navaratnam Dhasakumar S.
Published: February 2021

Reports have proposed a putative role for βV spectrin in outer hair cells (OHCs) of the cochlea. In an ongoing investigation of the role of the cytoskeleton in electromotility, we tested mice with a targeted exon deletion of βV spectrin (Spnb5), and unexpectedly find that Spnb5(-/-)animals’ auditory thresholds are unaffected. Similarly, these mice have normal OHC electromechanical activity (otoacoustic emissions) and non-linear capacitance. In contrast, magnitudes of auditory brainstem response (ABR) wave 1-amplitudes are significantly reduced. Evidence of a synaptopathy was absent with normal hair cell CtBP2 counts. In Spnb5(-/-)mice, the number of afferent and efferent nerve fibers is decreased. Consistent with this data, Spnb5 mRNA is present in Type I and II spiral ganglion neurons, but undetectable in OHCs. Together, these data establish that βV spectrin is important for hearing, affecting neuronal structure and function. Significantly, these data exclude βV spectrin as functionally important to OHCs as has been previously suggested.
A Reproducibility Analysis-based Statistical Framework for Residue-Residue Evolutionary Coupling Detection
Authors: Si Yunda , Zhang Yi , Yan Chengfei
Published: February 2021

Direct coupling analysis (DCA) has been widely used to infer evolutionary coupled residue pairs from the multiple sequence alignment (MSA) of homologous sequences. However, effectively selecting residue pairs with significant evolutionary couplings according to the result of DCA is a non-trivial task. In this study, we developed a general statistical framework for significant evolutionary coupling detection, referred to as IDR-DCA, which is based on reproducibility analysis of the coupling scores obtained from DCA on manually created MSA replicates. IDR-DCA was applied to select residue pairs for contact prediction for monomeric proteins, protein-protein interactions and monomeric RNAs, in which three different versions of DCA were applied. We demonstrated that with the application of IDR-DCA, the residue pairs selected using a universal threshold always yielded stable performance for contact prediction. Comparing with the application of carefully tuned coupling score cutoffs, IDR-DCA always showed better performance. The robustness of IDR-DCA was also supported through the MSA down-sampling analysis. We further demonstrated the effectiveness of applying constraints obtained from residue pairs selected by IDR-DCA to assist RNA secondary structure prediction.
LncRNA XIST knockdown suppresses cell proliferation and promotes apoptosis in diabetic cataract via miR-34a/SMAD2 axis
Authors: Wang Chao , Zhao Ruiling , Zhang Suhong
Published: February 2021

Emerging evidence has manifested that long non-coding RNAs (lncRNAs) played critical roles in diabetes. The present research aimed to investigate the role and mechanism of XIST on proliferation, migration and apoptosis in diabetic cataract (DC). In the present study, lens epithelial cells (SRA01/04) were treated by high glucose (HG). The levels of XIST, miR-34a and SMAD2 were examined by RT-qPCR. MTT, transwell, wound healing and TUNEL assays were employed to examine cell proliferation, invasion, migration and apoptosis. The interaction between miR-34a and XIST or SMAD2 was verified by luciferase reporter assay. It was found that XIST expression was increased and miR-34a level was decreased in DC tissues and HG-induced SRA01/04 cells. XIST knockdown or miR-34a addition attenuated cell proliferation and migration, and induced apoptosis in SRA01/04 cells under HG. XIST targeted miR-34a and regulated DC progression via miR-34a. SMAD2 was a target gene of miR-34a and was positively modulated by XIST. SMAD2 addition accelerated cell proliferation, migration and inhibited the apoptosis in HG-stimulated SRA01/04 cells, which were abrogated by XIST depletion. In conclusion, XIST facilitated the proliferation, migration and invasion, and inhibited the apoptosis via miR-34a/SMAD2 axis in DC.
Nelfinavir markedly improves lung pathology in SARS-CoV-2-infected Syrian hamsters despite lack of an antiviral effect
Authors: Foo Caroline S. , Abdelnabi Rana , Kaptein Suzanne J. F. , Zhang Xin , ter Horst Sebastiaan , Mols Raf , Delang Leen , Rocha-Pereira Joana , Coelmont Lotte , Leyssen Pieter , Dallmeier Kai , Vergote Valentijn , Heylen Elisabeth , Vangeel Laura , Chatterjee Arnab K. , Annaert Pieter , Augustijns Patrick , De Jonghe Steven , Jochmans Dirk , Weynand Birgit , Neyts Johan
Published: February 2021

In response to the ongoing COVID-19 pandemic, repurposing of drugs for the treatment of SARS-CoV-2 infections is being explored. The HIV protease inhibitor Nelfinavir, widely prescribed in combination with other HIV inhibitors, has been shown to inhibitin vitroSARS-CoV-2 replication. We here report on the effect of Nelfinavir in the Syrian hamster SARS-CoV-2 infection model. Although treatment of infected hamsters with either 15 or 50 mg/kg BID Nelfinavir [for four consecutive days, initiated on the day of infection] does not reduce viral RNA loads nor infectious virus titres in the lungs compared to the vehicle control, the drug reduced virus-induced lung pathology to nearly the baseline scores of healthy animals. A substantial interstitial infiltration of neutrophils is observed in the lungs of treated (both infected and uninfected) animals. The protective effect of Nelfinavir on SARS-CoV-2-induced lung pathology (at doses that are well tolerated and that result in exposures nearing those observed in HIV-infected patients) may lay the foundation for clinical studies with this widely used drug.
Sequential delivery of LAIV and SARS-CoV-2 in the ferret model can reduce SARS-CoV-2 shedding and does not result in enhanced lung pathology
Authors: Ryan Kathryn A. , Schewe Katarzyna E. , Crowe Jonathan , Fotheringham Susan A. , Hall Yper , Humphreys Richard , Marriott Anthony C. , Paterson Jemma , Rayner Emma , Salguero Francisco J. , Watson Robert J. , Whittaker Catherine J. , Carroll Miles W. , Dibben Oliver
Published: February 2021

Co-circulation of SARS-CoV-2 and influenza viruses could pose unpredictable risks to health systems globally, with recent studies suggesting more severe disease outcomes in co-infected patients. The lack of a readily available COVID-19 vaccine has reinforced the importance of influenza vaccine programmes during the COVID-19 pandemic. Live Attenuated Influenza Vaccine (LAIV) is an important tool in protecting against influenza, particularly in children. However, it is unknown whether LAIV administration might influence the outcomes of acute SARS-CoV-2 infection or disease. To investigate this, quadrivalent LAIV (QLAIV) was administered to ferrets 3 days pre- or post-SARS-CoV-2 infection. LAIV administration did not exacerbate SARS-CoV-2 disease course or lung pathology with either regimen. Additionally, LAIV administered prior to SARS-CoV-2 infection significantly reduced SARS-CoV-2 replication and shedding in the upper respiratory tract (URT). We conclude that LAIV administration in close proximity to SARS-CoV-2 infection does not exacerbate mild disease and can reduce SARS-CoV-2 shedding.
Synapomorphic variations in the THAP domains of the human THAP protein family and its homologs
Authors: Sanghavi Hiral M. , Majumdar Sharmistha
Published: February 2021

The THAP (Thanatos-associatedprotein) domain is a DNA-binding domain which binds DNA via a zinc coordinating C2CH motif. Although THAP domains share a conserved structural fold, they bind different DNA sequences in different THAP proteins which in turn perform distinct cellular functions. In this study, we investigate (using multiple sequence alignment,in silicomotif and secondary structure prediction) THAP domain conservation within the homologs of the human THAP (hTHAP) protein family. We report that there is significant variation in sequence and predicted secondary structure elements across hTHAP homologs. Interestingly, we report that the THAP domain can be either longer or shorter than the conventional 90 residues and the amino terminal C2CH motif within the THAP domain serves as a hotspot for insertion or deletion. Our results lay the foundation for future studies which will further our understanding of the evolution of THAP domain and regulation of its function.
MDA5 autoimmune disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA
Authors: Yu Qin , del Valle Alba Herrero , Singh Rahul , Modis Yorgo
Published: February 2021

Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The ATPase activity of MDA5 contributes to its dsRNA binding selectivity. Mutations that reduce RNA selectivity can cause autoimmune disease. Here, we show how the disease-associated MDA5 variant M854K perturbs MDA5-dsRNA recognition. M854K MDA5 constitutively activates interferon signaling in the absence of exogenous RNA. M854K MDA5 lacks ATPase activity and binds more tightly to synthetic Alu:Alu dsRNA. CryoEM structures MDA5-dsRNA filaments at different stages of ATP hydrolysis show that the K854 side-chain forms polar bonds that constrain the conformation of MDA5 subdomains, disrupting key steps in the ATPase cycle-RNA footprint expansion and helical twist modulation. The M854K mutation inhibits ATP-dependent RNA proofreading via a novel allosteric mechanism, allowing MDA5 to form signaling complexes on endogenous RNAs. This work provides new insights on how MDA5 recognizes dsRNA in health and disease.
Long noncoding RNAVENTHEARTis required for cardiomyocyte specification and function
Authors: Dashi Albert , Tan Wilson L.W. , Anene-Nzelu Chukwuemeka George , Pan Bangfen , Ilmari Autio Matias , Tiang Zenia , Hartman Robin J.G. , Stenzig Justus , Wei Heming , Bin Chen Gao , Ackers-Johnson Matthew Andrew , Lim Bing , Walentinsson Anna , Iyer Vidhya Vardharajan , Jonsson Malin K.B. , Foo Roger S.
Published: February 2021

Rationale

Long noncoding RNAs (lncRNAs) control cardiac gene expression during heart development and disease. It is accordingly plausible for the same lncRNA to regulate both cardiac development, as well as play a role in adult heart disease progression. lncRNA regulators of early cardiomyocyte (CM) lineage commitment have been identified and characterised, however those controlling later CM specification remain unknown.

Objectives

In this study we identified a novel lncRNA required for CM specification, maturation and function, and also discovered its suggested relevance to heart disease.

Methods and Results

We performed single cell RNA-seq on human embryonic stem cell derived cardiomyocytes at 2, 6 and 12 weeks of differentiation. Weighted correlation network analysis (WGCNA) identified core gene modules, including lncRNAs highly abundant and uniquely expressed in the human heart. A lncRNA (we callVENTHEART,VHRT) co-expressed with cardiac maturation and ventricular-specific genesMYL2andMYH7, as well as in adult human ventricular tissue. CRISPR-mediated excision ofVHRTled to impaired CM sarcomere formation, and loss of the CM specification gene program.VHRTknockdown (KD) in hESC-CMs confirmed its regulatory role for key cardiac contraction, calcium hemostasis and heart development genes, includingMYH6andRYR2. Functional evaluation afterVHRTKD using impedance-based technology and action potential recordings, proved reduced contraction amplitude and loss of the ventricular-like action potential in CM, respectively. Through an integrative analysis of genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) and gene co-expression network, we foundVHRTto be co-regulated with core cardiac contractile genes, and the likely source of a heart failure genetic association signal overlapping theVHRTgene locus. Finally,VHRTKD and human failing heart transcriptome comparison validates the consistent downregulation again of cardiac contractile and calcium regulatory genes (P<0.05).

Conclusion

We conclude thatVHRTlncRNA is required for proper CM specification and function. Furthermore, reducedVHRTmay contribute to the development or progression of human heart disease.
Evidence for efficient non-evaporative leaf-to-air heat dissipation in a pine forest under drought conditions
Authors: Muller Jonathan D. , Rotenberg Eyal , Tatarinov Fyodor , Oz Itay , Yakir Dan
Published: February 2021

Drier climates predicted for many regions can result in reduced evaporative cooling leading to leaf heat stress and enhanced mortality. To what extent non-evaporative cooling can contribute to plant resilience to the increasingly stressful conditions is poorly known at present.

Using a novel, high accuracy infrared system for continuous measurements of leaf temperature in mature trees under field conditions, we assessed leaf-to-air temperature differences ΔTleaf−airof pine needles during drought.

On mid-summer days, ΔTleaf−airremained <1.5 °C, both in trees exposed to summer drought, and in those provided with a supplement irrigation having a 10× higher transpiration rate. The non-evaporative cooling in the drought-exposed trees must be facilitated by low resistance to heat transfer generating largeH. ΔTleaf−airwas weakly related to variations in the radiation load and mean wind speed in the lower part of the canopy, but highly dependent on canopy structure and within-canopy turbulence that enhanced the sensible heat fluxH.

Non-evaporative cooling is demonstrated as an effective cooling mechanism in needle-leaf trees, which can be a critical factor in forest resistance to drying climates. The generation of a largeHat the leaf scale provides a basis for the development of the previously identified canopy-scale ‘convector effect’.
Geometry of neural computation unifies working memory and planning
Authors: Ehrlich Daniel B. , Murray John D.
Published: February 2021

Real-world tasks require coordination of working memory, decision making, and planning, yet these cognitive functions have disproportionately been studied as independent modular processes in the brain. Here we propose that contingency representations, defined as mappings for how future behaviors depend on upcoming events, can unify working memory and planning computations. We designed a task capable of disambiguating distinct types of representations. Our experiments revealed that human behavior is consistent with contingency representations, and not with traditional sensory models of working memory. In task-optimized recurrent neural networks we investigated possible circuit mechanisms for contingency representations and found that these representations can explain neurophysiological observations from prefrontal cortex during working memory tasks. Finally, we generated falsifiable predictions for neural data to identify contingency representations in neural data and to dissociate different models of working memory. Our findings characterize a neural representational strategy that can unify working memory, planning, and context-dependent decision making.
Host PDZ-containing proteins targeted by SARS-Cov-2
Authors: Caillet-Saguy Célia , Durbesson Fabien , Rezelj Veronica V. , Gogl Gergö , Tran Quang Dinh , Twizere Jean-Claude , Vignuzzi Marco , Vincentelli Renaud , Wolff Nicolas
Published: February 2021

Small linear motif targeting protein interacting domains called PDZ have been identified at the C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins E, 3a, and N. Using a high-throughput approach of affinity-profiling against the full human PDZome, we identified sixteen human PDZ binders of SARS-CoV-2 proteins E, 3A and N showing significant interactions with dissociation constants values ranging from 3 μM to 82 μM. Six of them (TJP1, PTPN13, HTRA1, PARD3, MLLT4, LNX2) are also recognized by SARS-CoV while three (NHERF1, MAST2, RADIL) are specific to SARS-CoV-2 E protein. Most of these SARS-CoV-2 protein partners are involved in cellular junctions/polarity and could be also linked to evasion mechanisms of the immune responses during viral infection. Seven of the PDZ-containing proteins among binders of the SARS-CoV-2 proteins E, 3a or N affect significantly viral replication under knock-down gene expression in infected cells. This PDZ profiling identifying human proteins potentially targeted by SARS-CoV-2 can help to understand the multifactorial severity of COVID19 and to conceive effective anti-coronaviral agents for therapeutic purposes.
Enhanced immunogenicity of a synthetic DNA vaccine expressing consensus SARS-CoV-2 Spike protein using needle-free immunization
Authors: Alamri Sawsan S , Alluhaybi Khalid A , Alhabbab Rowa Y , Algaissi Abdullah , Almahboub Sarah , Alfaleh Mohamed A , Abujamel Turki S , Abdulaal Wesam , ElAssouli M-Zaki , Alharbi Rahaf , Hassanain Mazen , Hashem Anwar M
Published: February 2021

The ongoing global pandemic of Coronavirus Disease 2019 (COVID-19) calls for an urgent development of effective and safe prophylactic and therapeutic measures. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) glycoprotein is a major immunogenic and protective protein, and plays a crucial role in viral pathogenesis. In this study, we successfully constructed a synthetic codon-optimized DNA-based vaccine as a countermeasure against SARS-CoV-2; denoted as VIU-1005. The design was based on the synthesis of codon-optimized coding sequence for optimal mammalian expression of a consensus full-length S glycoprotein. The successful construction of the vaccine was confirmed by restriction digestion and sequencing, and the protein expression of the S protein was confirmed by western blot and immunofluorescence staining in mammalian cells. The immunogenicity of the vaccine was tested in two mouse models (BALB/c and C57BL/6J). Th1-skewed systemic S-specific IgG antibodies and neutralizing antibodies (nAbs) were significantly induced in both models four weeks post three injections with 100 μg of the VIU-1005 vaccine via intramuscular needle injection but not intradermal or subcutaneous routes. Importantly, such immunization induced long-lasting IgG response in mice that lasted for at least 6 months. Interestingly, using a needle-free system, we showed an enhanced immunogenicity of VIU-1005 in which lower doses such as 25-50 μg or less number of doses were able to elicit significantly high levels of Th1-biased systemic S-specific IgG antibodies and nAbs via intramuscular immunization compared to needle immunization. Compared to the intradermal needle injection which failed to induce any significant immune response, intradermal needle-free immunization elicited robust Th1-biased humoral response similar to that observed with intramuscular immunization. Furthermore, immunization with VIU-1005 induced potent S-specific cellular response as demonstrated by the significantly high levels of IFN-γ, TNF and IL-2 cytokines production in memory CD8+and CD4+T cells in BALB/c mice. Together, our results demonstrate that the synthetic VIU-1005 candidate DNA vaccine is highly immunogenic and capable of inducing long-lasting and Th1-skewed immune response in mice. Furthermore, we show that the use of needle-free system could enhance the immunogenicity and minimize doses needed to induce protective immunity in mice, supporting further preclinical and clinical testing of this candidate vaccine.
Predictors for readmission due to cellulitis among Japanese patients
Authors: Norimatsu Yuta , Ohno Yuki
Published: February 2021

Cellulitis is an infection of the soft tissues of the skin. Some patients are hospitalized multiple times; lymphedema, chronic venous insufficiency, peripheral circulatory disturbance, and deep vein thrombosis are said to be risk factors for multiple admissions. Conversely, in Japan, elderly women and undernourished elderly have been reported to be at risk of multiple hospitalizations, suggesting a different patient background from that reported overseas. We investigated the characteristics of readmission cases for patients hospitalized for cellulitis in Japan. We retrospectively examined cases of cellulitis and erysipelas admitted between April 1, 2005 and March 31, 2018. Patients with cellulitis or erysipelas at multiple sites and those with osteomyelitis, pressure ulcer infection, and necrotizing fasciitis were excluded. In terms of recurrence, only hospitalizations for recurrence at the same site were considered. Patients with multiple hospitalizations had significantly lower blood albumin levels than those hospitalized only once. Furthermore, the rates of lymphedema, hypertension, and hyperlipidemia were significantly higher in patients hospitalized multiple times. Other laboratory and clinical factors were not statistically significant. Therefore, hypoalbuminemia with or without liver dysfunction, lymphedema, hypertension, and hyperlipidemia were suggested as risk factors for cellulitis recurrence. However, chronic venous insufficiency, peripheral circulatory disturbance, and deep vein thrombosis did not seem to be risk factors in Japanese cases. Japanese cases had a low body mass index (approximately 25 kg/m2), suggesting that the patient background may be different from that in existing reports. This suggests that the risk factors in Japanese cases may be different from those reported in other countries.