Functional landscape of SARS-CoV-2 cellular restriction.

A deficient interferon (IFN) response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been implicated as a determinant of severe coronavirus disease 2019 (COVID-19). To identify the molecular effectors that govern IFN control of SARS-CoV-2 infection, we conducted a large-scale gain-of-function analysis that evaluated the impact of human IFN-stimulated genes (ISGs) on viral replication. A limited subset of ISGs were found to control viral infection, including endosomal factors inhibiting viral entry, RNA binding proteins suppressing viral RNA synthesis, and a highly enriched cluster of endoplasmic reticulum (ER)/Golgi-resident ISGs inhibiting viral assembly/egress. These included broad-acting antiviral ISGs and eight ISGs that specifically inhibited SARS-CoV-2 and SARS-CoV-1 replication. Among the broad-acting ISGs was BST2/tetherin, which impeded viral release and is antagonized by SARS-CoV-2 Orf7a protein. Overall, these data illuminate a set of ISGs that underlie innate immune control of SARS-CoV-2/SARS-CoV-1 infection, which will facilitate the understanding of host determinants that impact disease severity and offer potential therapeutic strategies for COVID-19.

A multi-scale map of cell structure fusing protein images and interactions.

The cell is a multi-scale structure with modular organization across at least four orders of magnitude1. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are typically treated separately2,3. Here we integrate immunofluorescence images in the Human Protein Atlas4 with affinity purifications in BioPlex5 to create a unified hierarchical map of human cell architecture. Integration is achieved by configuring each approach as a general measure of protein distance, then calibrating the two measures using machine learning. The map, known as the multi-scale integrated cell (MuSIC 1.0), resolves 69 subcellular systems, of which approximately half are to our knowledge undocumented. Accordingly, we perform 134 additional affinity purifications and validate subunit associations for the majority of systems. The map reveals a pre-ribosomal RNA processing assembly and accessory factors, which we show govern rRNA maturation, and functional roles for SRRM1 and FAM120C in chromatin and RPS3A in splicing. By integration across scales, MuSIC increases the resolution of imaging while giving protein interactions a spatial dimension, paving the way to incorporate diverse types of data in proteome-wide cell maps.

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.

MOTIVATION: The investigation of sets of genes using biological pathways is a common task for researchers and is supported by a wide variety of software tools. This type of analysis generates hypotheses about the biological processes that are active or modulated in a specific experimental context. RESULTS: The Network Data Exchange Integrated Query (NDEx IQuery) is a new tool for network and pathway-based gene set interpretation that complements or extends existing resources. It combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results. The NDEx IQuery web application performs multiple gene set analyses based on diverse pathways and networks stored in NDEx. These include curated pathways from WikiPathways and SIGNOR, published pathway figures from the last 27 years, machine-assembled networks using the INDRA system, and the new NCI-PID v2.0, an updated version of the popular NCI Pathway Interaction Database. NDEx IQuery's integration with MSigDB and cBioPortal now provides pathway analysis in the context of these two resources. AVAILABILITY AND IMPLEMENTATION: NDEx IQuery is available at https://www.ndexbio.org/iquery and is implemented in Javascript and Java.

A therapeutic convection-enhanced macroencapsulation device for enhancing ß cell viability and insulin secretion.

Islet transplantation for type 1 diabetes treatment has been limited by the need for lifelong immunosuppression regimens. This challenge has prompted the development of macroencapsulation devices (MEDs) to immunoprotect the transplanted islets. While promising, conventional MEDs are faced with insufficient transport of oxygen, glucose, and insulin because of the reliance on passive diffusion. Hence, these devices are constrained to two-dimensional, wafer-like geometries with limited loading capacity to maintain cells within a distance of passive diffusion. We hypothesized that convective nutrient transport could extend the loading capacity while also promoting cell viability, rapid glucose equilibration, and the physiological levels of insulin secretion. Here, we showed that convective transport improves nutrient delivery throughout the device and affords a three-dimensional capsule geometry that encapsulates 9.7-fold-more cells than conventional MEDs. Transplantation of a convection-enhanced MED (ceMED) containing insulin-secreting ß cells into immunocompetent, hyperglycemic rats demonstrated a rapid, vascular-independent, and glucose-stimulated insulin response, resulting in early amelioration of hyperglycemia, improved glucose tolerance, and reduced fibrosis. Finally, to address potential translational barriers, we outlined future steps necessary to optimize the ceMED design for long-term efficacy and clinical utility.

CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method.

Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.

CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing.

Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.

The role of anticoagulation for superior sagittal sinus thrombosis following craniotomy for resection of parasagittal/parafalcine meningiomas.

OBJECTIVE: The safety and efficacy of anticoagulation in managing superior sagittal sinus (SSS) thrombosis remains unclear. The present study investigated the relationship between anticoagulation and cerebrovascular complications in parasagittal/parafalcine meningioma patients presenting with post-surgical SSS thrombosis. METHODS: We analyzed 266 patients treated at a single institution between 2005 and 2020. Bivariate analysis was conducted using the Mann-Whitney U test and Fisher's exact test. Multivariate analysis was conducted using a logistic regression model. Blood thinning medications investigated included aspirin, warfarin, heparin, apixaban, rivaroxaban, and other novel oral anticoagulants (NOACs). A symptomatic SSS thrombosis was defined as a radiographically apparent thrombosis with new headaches, seizures, altered sensorium, or neurological deficits. RESULTS: Our patient cohort was majority female (67.3%) with a mean age ([Formula: see text] SD) of 58.82 [Formula: see text] 13.04 years. A total of 15 (5.6%) patients developed postoperative SSS thrombosis and 5 (1.9%) were symptomatic; 2 (0.8%) symptomatic patients received anticoagulation. None of these 15 patients developed cerebrovascular complications following observation or anticoagulative treatment of asymptomatic SSS thrombosis. While incidence of any other postoperative complications was significantly associated with SSS thrombosis in bivariate analysis (p = 0.015), this association was no longer observed in multivariate analysis (OR = 2.15, p = 0.16) when controlling for patient age, sex, and anatomical location of the tumor along the SSS. CONCLUSIONS: Our single-institution study examining the incidence of SSS thrombosis and associated risk factors highlights the need for further research efforts better prognosticate this adverse outcome. Conservative management may represent a viable treatment strategy for patients with SSS thrombosis.

Nanowire Chemical/Biological Sensors: Status and a Roadmap for the Future.

Chemiresistive sensors are becoming increasingly important as they offer an inexpensive option to conventional analytical instrumentation, they can be readily integrated into electronic devices, and they have low power requirements. Nanowires (NWs) are a major theme in chemosensor development. High surface area, interwire junctions, and restricted conduction pathways give intrinsically high sensitivity and new mechanisms to transduce the binding or action of analytes. This Review details the status of NW chemosensors with selected examples from the literature. We begin by proposing a principle for understanding electrical transport and transduction mechanisms in NW sensors. Next, we offer the reader a review of device performance parameters. Then, we consider the different NW types followed by a summary of NW assembly and different device platform architectures. Subsequently, we discuss NW functionalization strategies. Finally, we propose future developments in NW sensing to address selectivity, sensor drift, sensitivity, response analysis, and emerging applications.

Chemiresistive Sensor Arrays from Conductive 2D Metal-Organic Frameworks.

Applications of porous metal-organic frameworks (MOFs) in electronic devices are rare, owing in large part to a lack of MOFs that display electrical conductivity. Here, we describe the use of conductive two-dimensional (2D) MOFs as a new class of materials for chemiresistive sensing of volatile organic compounds (VOCs). We demonstrate that a family of structurally analogous 2D MOFs can be used to construct a cross-reactive sensor array that allows for clear discrimination between different categories of VOCs. Experimental data show that multiple sensing mechanisms are operative with high degrees of orthogonality, establishing that the 2D MOFs used here are mechanistically unique and offer advantages relative to other known chemiresistor materials.

The Ratio of Free to Bound Desmosine and Isodesmosine May Reflect Emphysematous Changes in COPD.

BACKGROUND: The unique elastin crosslinks, desmosine and isodesmosine (DID) are significantly elevated in blood, urine, and sputum from patients with COPD, and may decline following treatment of the disease. However, the large degree of variance in this biomarker among COPD patients with similar levels of disease suggests that it has limited prognostic value with regard to the degree of lung disease in a given individual. As an alternative to measuring the total amount of DID, we propose using the ratio of free to peptide-bound DID, which may provide a better indication of overall lung disease. METHODS: To test this hypothesis, the free/bound DID ratio was measured in bronchoalveolar lavage fluid (BALF) from both hamsters with elastase-induced emphysema and controls not given the enzyme, using a combination of liquid chromatography and tandem mass spectroscopy. This ratio was then correlated with airspace enlargement, as measured by the mean percentage of lung surface area at ×100 microscopic magnification. RESULTS: There was a significant negative correlation between the free/bound DID ratio in BALF and lung surface area. However, there was no correlation between this ratio and total BALF DID, suggesting that free/bound DID is unrelated to the immediate rate of breakdown of elastic fibers, and may instead measure the cumulative effect of elastase injury in the lung. CONCLUSIONS: The free/bound DID ratio may be a useful measure of emphysematous changes in the lung and might also serve as a screening procedure for healthy smokers and other individuals at risk for developing COPD.

New therapy in cardioprotection.

PURPOSE OF REVIEW: An increasing number of patients are presenting for major surgery with cardiovascular comorbidities. Evidence of myocardial injury was found in 8% of all noncardiac surgery patients older than 45 years and was associated with adverse outcome. For this reason, there has been a lot of interest in finding and evaluating effective cardioprotective interventions. RECENT FINDINGS: Current evidence suggests that statins, volatile anesthetic agents, and propofol are cardioprotective. Beta blockers reduce myocardial injury, but the resultant hypotension may contribute to the increased all-cause mortality and stroke risk seen. Likewise, alpha 2 agonists can be a cause of cardiac injury if hypotension is not promptly managed. Continuation of aspirin perioperatively can increase the risk of major bleeding with or without the benefit of reduced myocardial risk. Contrary to the initial Evaluation of Nitrous Oxide in the Gas Mixture for Anaesthesia study, nitrous oxide does not seem to increase the risk of myocardial injury. SUMMARY: It is recommended that patients already on statins or beta blockers should have them continued perioperatively. If beta blockers are initiated, the dose should be titrated to heart rate and blood pressure. The decision regarding continuation of aspirin should be on a case-to-case basis based on patient and surgical risk factors.

Single-walled carbon nanotube/metalloporphyrin composites for the chemiresistive detection of amines and meat spoilage.

Chemiresistive detectors for amine vapors were made from single-walled carbon nanotubes by noncovalent modification with cobalt meso-arylporphyrin complexes. We show that through changes in the oxidation state of the metal, the electron-withdrawing character of the porphyrinato ligand, and the counteranion, the magnitude of the chemiresistive response to ammonia could be improved. The devices exhibited sub-ppm sensitivity and high selectivity toward amines as well as good stability to air, moisture, and time. The application of these chemiresistors in the detection of various biogenic amines (i.e. putrescine, cadaverine) and in the monitoring of spoilage in raw meat and fish samples (chicken, pork, salmon, cod) over several days was also demonstrated.

Cu3(hexaiminotriphenylene)2: an electrically conductive 2D metal-organic framework for chemiresistive sensing.

The utility of metal-organic frameworks (MOFs) as functional materials in electronic devices has been limited to date by a lack of MOFs that display high electrical conductivity. Here, we report the synthesis of a new electrically conductive 2D MOF, Cu3(HITP)2 (HITP=2,3,6,7,10,11-hexaiminotriphenylene), which displays a bulk conductivity of 0.2 S cm(-1) (pellet, two-point-probe). Devices synthesized by simple drop casting of Cu3(HITP)2 dispersions function as reversible chemiresistive sensors, capable of detecting sub-ppm levels of ammonia vapor. Comparison with the isostructural 2D MOF Ni3(HITP)2 shows that the copper sites are critical for ammonia sensing, indicating that rational design/synthesis can be used to tune the functional properties of conductive MOFs.

Investigation of AFeO3 (A=Ba, Sr) Perovskites for the Oxidative Dehydrogenation of Light Alkanes under Chemical Looping Conditions.

Oxidative dehydrogenation (ODH) of light alkanes to produce C2-C3 olefins is a promising alternative to conventional steam cracking. Perovskite oxides are emerging as efficient catalysts for this process due to their unique properties such as high oxygen storage capacity (OSC), reversible redox behavior, and tunability. Here, we explore AFeO3 (A=Ba, Sr) bulk perovskites for the ODH of ethane and propane under chemical looping conditions (CL-ODH). The higher OSC and oxygen mobility of SrFeO3 perovskite contributed to its higher activity but lower olefin selectivity than its Ba counterpart. However, SrFeO3 perovskite is superior in terms of cyclic stability over multiple redox cycles. Transformations of the perovskite to reduced phases including brownmillerite A2Fe2O5 were identified by X-ray diffraction (XRD) as a cause of performance degradation, which was fully reversible upon air regeneration. A pre-desorption step was utilized to selectively tune the amount of lattice oxygen as a function of temperature and dwell time to enhance olefin selectivity while suppressing CO2 formation from the deep oxidation of propane. Overall, SrFeO3 exhibits promising potential for the CL-ODH of light alkanes, and optimization through surface and structural modifications may further engineer well-regulated lattice oxygen for maximizing olefin yield.

Transtympanic delivery of V2O5 nanowires with a tympanic-membrane penetrating peptide.

Otitis media is a prevalent pediatric condition. Local delivery of antimicrobial agents to treat otitis media is hindered by the low permeability of the stratum corneum layer in the tympanic membrane. While nanozymes, often inorganic nanoparticles, have been developed to cure otitis media in an antibiotic-free manner in a chinchilla animal model, the tympanic membrane creates an impenetrable barrier that prevents the local and non-invasive delivery of nanozymes. Here, we use a newly developed vanadium pentoxide (V2O5) nanowire as an example, which catalyzes the metabolic products of an otitis media pathogen (Streptococcus pneumoniae) into antiseptics, to explore the transtympanic delivery strategies for antimicrobial nanozymes. V2O5 nanowires with smaller dimensions (<300 nm in length) were synthesized by optimizing the synthesis conditions. To enhance penetrations across intact tympanic membranes, the nanowire was mixed or surface-modified with a trans-tympanic peptide, TMT3. The peptide-modified nanowires were characterized for their physical properties, catalytic activities, and antimicrobial activities. The cytotoxicity profile and permeation across ex vivo tympanic membrane samples were analyzed for the mixed and surface-modified nanozyme formulations.

A Pseudo-Surfactant Chemical Permeation Enhancer to Treat Otitis Media via Sustained Transtympanic Delivery of Antibiotics.

Chemical permeation enhancers (CPEs) represent a prevalent and safe strategy to enable noninvasive drug delivery across skin-like biological barriers such as the tympanic membrane (TM). While most existing CPEs interact strongly with the lipid bilayers in the stratum corneum to create defects as diffusion paths, their interactions with the delivery system, such as polymers forming a hydrogel, can compromise gelation, formulation stability, and drug diffusion. To overcome this challenge, differing interactions between CPEs and the hydrogel system are explored, especially those with sodium dodecyl sulfate (SDS), an ionic surfactant and a common CPE, and those with methyl laurate (ML), a nonionic counterpart with a similar length alkyl chain. Notably, the use of ML effectively decouples permeation enhancement from gelation, enabling sustained delivery across TMs to treat acute otitis media (AOM), which is not possible with the use of SDS. Ciprofloxacin and ML are shown to form a pseudo-surfactant that significantly boosts transtympanic permeation. The middle ear ciprofloxacin concentration is increased by 70-fold in vivo in a chinchilla AOM model, yielding superior efficacy and biocompatibility than the previous highest-performing formulation. Beyond improved efficacy and biocompatibility, this single-CPE formulation significantly accelerates its progression toward clinical deployment.

Assembly and analysis of the genome of Notholithocarpus densiflorus.

Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes, and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.), phylogenetic analysis has determined that the tanoak is an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with a single species. These trees are highly susceptible to "sudden oak death" (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread deaths of tanoaks. In this study, we set out to assemble the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD. First, we sequenced and de novo assembled a draft reference genome of N. densiflorus using cobarcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore long reads to 30× coverage. To our knowledge, the draft genome reported here is one of the more contiguous and complete genomes of a tree species published to date, with a contig N50 of ∼1.2 Mb, a scaffold N50 of ∼2.1 Mb, and a complete gene score of 95.5% through BUSCO analysis. In addition, we sequenced 11 genetically distinct individuals and mapped these onto the draft reference genome, enabling the discovery of almost 25 million single nucleotide polymorphisms and ∼4.4 million small insertions and deletions. Finally, using cobarcoded data, we were able to generate a complete haplotype coverage of all 11 genomes.

Comprehensive analysis of geographic and breed-purpose influences on genetic diversity and inherited disease risk in the Doberman dog breed.

BACKGROUND: Publicly available phenotype data and genotyping array data from two citizen science projects: "Doberman Health Surveys" and "The Doberman Diversity Project" were analyzed to explore relative homozygosity, diversity, and disorder risk according to geographical locale and breeding purpose in the Doberman. RESULTS: From the phenotypic data cohort, life expectancy of a Doberman at birth is 9.1 years. The leading causes of death were heart disease (accounting for 28% of deaths) and cancers (collectively accounting for 14% of deaths). By genotyping, the world Doberman population exists as four major cohorts (European exhibition-bred, Americas exhibition-bred, European work, Americas pet/informal). Considering the entire Doberman population, four genomic regions longer than 500 Kb are fixed in 90% or more of 3,226 dogs included in this study. The four fixed regions reside on two autosomal chromosomes: CFA3:0.8-2.3 Mb (1.55 Mb); CFA3: 57.9-59.8 Mb (1.8 Mb); CFA31:0-1.2 Mb (1.2 Mb); and CFA31:4.80-6.47 Mb (1.67 Mb). Using public variant call files including variants for eight Doberman pinschers, we observed 30 potentially functional alternate variants that were evolutionarily diverged relative to the wider sequenced dog population within the four strongly homozygous chromosomal regions. Effective population size (Ne) is a statistical measure of breed diversity at the time of sampling that approximates the number of unique individuals. The major identified sub-populations of Dobermans demonstrated Ne in the range 70-236. The mean level of inbreeding in the Doberman breed is 40% as calculated by the number of array variants in runs of homozygosity divided by the assayed genome size (excluding the X chromosome). The lowest observed level of inbreeding in the Dobermans assayed was 15% in animals that were first generation mixes of European and USA bred Dobermans. Array variant analysis shows that inter-crossing between European and USA-bred Dobermans has capacity to re-introduce variation at many loci that are strongly homozygous. CONCLUSIONS: We conclude that efforts to improve breed diversity first should focus on regions with the highest fixation levels, but managers must ensure that mutation loads are not worsened by increasing the frequencies of rarer haplotypes in the identified regions. The analysis of global data identified regions of strong fixation that might impact known disorder risks in the breed. Plausible gene candidates for future analysis of the genetic basis of cardiac disease and cancer were identified in the analysis.

Review of meningioma diagnosis and management.

Meningiomas are the most common intracranial tumors in adult patients. Although the majority of meningiomas are diagnosed as benign, approximately 20% of cases are high-grade tumors that require significant clinical treatment. The gold standard for grading central nervous system tumors comes from the World Health Organization Classification of Tumors of the central nervous system. Treatment options also depend on the location, imaging, and histopathological features of the tumor. This review will cover diagnostic strategies for meningiomas, including 2021 updates to the World Health Organization's grading of meningiomas. Meningioma treatment plans are variable and highly dependent on tumor grading. This review will also update the reader on developments in the treatment of meningiomas, including surgery, radiation therapy and monoclonal antibody treatment.

Recurrent meningioma: When to intervene.

Meningioma occurs most frequently as a benign tumor central nervous system that is common in old females. Radiation exposure and deletion of the NF2 gene are known risk factors. However, there is no consensus about the role of sex hormones. Meningiomas are usually benign tumors, but 6% can be anaplastic or atypical. Most asymptomatic patients do not require treatment, but complete surgical resection is recommended for symptomatic patients. If a tumor returns after being resected previously, it is recommended to be resected, followed by radiotherapy in some cases. Meningiomas (benign, atypical, and malignant) recurring after standard treatment fails could be treated with hormone therapy, chemotherapy, target therapy, and calcium channel blockers.