Showing papers by "Washington State University published in 2021"

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

A ubiquitous tire rubber–derived chemical induces acute mortality in coho salmon

Abstract: In U.S. Pacific Northwest coho salmon (Oncorhynchus kisutch), stormwater exposure annually causes unexplained acute mortality when adult salmon migrate to urban creeks to reproduce. By investigating this phenomenon, we identified a highly toxic quinone transformation product of N-(1,3-dimethylbutyl)-N9-phenyl-p-phenylenediamine) (6PPD), a globally ubiquitous tire rubber antioxidant. Retrospective analysis of representative roadway runoff and stormwater-impacted creeks of the U.S. West Coast indicated widespread occurrence of 6PPD-quinone (

Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody.

Abstract: The recurrent zoonotic spillover of coronaviruses (CoVs) into the human population underscores the need for broadly active countermeasures. We employed a directed evolution approach to engineer three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies for enhanced neutralization breadth and potency. One of the affinity-matured variants, ADG-2, displays strong binding activity to a large panel of sarbecovirus receptor binding domains and neutralizes representative epidemic sarbecoviruses with high potency. Structural and biochemical studies demonstrate that ADG-2 employs a distinct angle of approach to recognize a highly conserved epitope that overlaps the receptor binding site. In immunocompetent mouse models of SARS and COVID-19, prophylactic administration of ADG-2 provided complete protection against respiratory burden, viral replication in the lungs, and lung pathology. Altogether, ADG-2 represents a promising broad-spectrum therapeutic candidate against clade 1 sarbecoviruses.

A trade-off between plant and soil carbon storage under elevated CO2.

Abstract: Terrestrial ecosystems remove about 30 per cent of the carbon dioxide (CO2) emitted by human activities each year1, yet the persistence of this carbon sink depends partly on how plant biomass and soil organic carbon (SOC) stocks respond to future increases in atmospheric CO2 (refs. 2,3). Although plant biomass often increases in elevated CO2 (eCO2) experiments4–6, SOC has been observed to increase, remain unchanged or even decline7. The mechanisms that drive this variation across experiments remain poorly understood, creating uncertainty in climate projections8,9. Here we synthesized data from 108 eCO2 experiments and found that the effect of eCO2 on SOC stocks is best explained by a negative relationship with plant biomass: when plant biomass is strongly stimulated by eCO2, SOC storage declines; conversely, when biomass is weakly stimulated, SOC storage increases. This trade-off appears to be related to plant nutrient acquisition, in which plants increase their biomass by mining the soil for nutrients, which decreases SOC storage. We found that, overall, SOC stocks increase with eCO2 in grasslands (8 ± 2 per cent) but not in forests (0 ± 2 per cent), even though plant biomass in grasslands increase less (9 ± 3 per cent) than in forests (23 ± 2 per cent). Ecosystem models do not reproduce this trade-off, which implies that projections of SOC may need to be revised. A synthesis of elevated carbon dioxide experiments reveals that when plant biomass is strongly stimulated by elevated carbon dioxide levels, soil carbon storage declines, and where biomass is weakly stimulated, soil carbon accumulates.

A gravitational-wave measurement of the Hubble constant following the second observing run of Advanced LIGO and Virgo

Abstract: This paper presents the gravitational-wave measurement of the Hubble constant (H 0) using the detections from the first and second observing runs of the Advanced LIGO and Virgo detector network. The presence of the transient electromagnetic counterpart of the binary neutron star GW170817 led to the first standard-siren measurement of H 0. Here we additionally use binary black hole detections in conjunction with galaxy catalogs and report a joint measurement. Our updated measurement is H 0 = km s−1 Mpc−1 (68.3% of the highest density posterior interval with a flat-in-log prior) which is an improvement by a factor of 1.04 (about 4%) over the GW170817-only value of km s−1 Mpc−1. A significant additional contribution currently comes from GW170814, a loud and well-localized detection from a part of the sky thoroughly covered by the Dark Energy Survey. With numerous detections anticipated over the upcoming years, an exhaustive understanding of other systematic effects are also going to become increasingly important. These results establish the path to cosmology using gravitational-wave observations with and without transient electromagnetic counterparts.

2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Abstract: In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Low-PGM and PGM-Free Catalysts for Proton Exchange Membrane Fuel Cells: Stability Challenges and Material Solutions.

Abstract: Fuel cells as an attractive clean energy technology have recently regained popularity in academia, government, and industry. In a mainstream proton exchange membrane (PEM) fuel cell, platinum-group-metal (PGM)-based catalysts account for ≈50% of the projected total cost for large-scale production. To lower the cost, two materials-based strategies have been pursued: 1) to decrease PGM catalyst usage (so-called low-PGM catalysts), and 2) to develop alternative PGM-free catalysts. Grand stability challenges exist when PGM catalyst loading is decreased in a membrane electrode assembly (MEA)-the power generation unit of a PEM fuel cell-or when PGM-free catalysts are integrated into an MEA. More importantly, there is a significant knowledge gap between materials innovation and device integration. For example, high-performance electrocatalysts usually demonstrate undesired quick degradation in MEAs. This issue significantly limits the development of PEM fuel cells. Herein, recent progress in understanding the degradation of low-PGM and PGM-free catalysts in fuel cell MEAs and materials-based solutions to address these issues are reviewed. The key factors that degrade the MEA performance are highlighted. Innovative, emerging material concepts and development of low-PGM and PGM-free catalysts are discussed.

Characterization of SARS-CoV-2 RNA, Antibodies, and Neutralizing Capacity in Milk Produced by Women with COVID-19.

Abstract: Whether mother-to-infant SARS-CoV-2 transmission can occur during breastfeeding and, if so, whether the benefits of breastfeeding outweigh this risk during maternal COVID-19 illness remain important questions Using RT-qPCR, we did not detect SARS-CoV-2 RNA in any milk sample (n = 37) collected from 18 women following COVID-19 diagnosis Although we detected evidence of viral RNA on 8 out of 70 breast skin swabs, only one was considered a conclusive positive result In contrast, 76% of the milk samples collected from women with COVID-19 contained SARS-CoV-2-specific IgA, and 80% had SARS-CoV-2-specific IgG In addition, 62% of the milk samples were able to neutralize SARS-CoV-2 infectivity in vitro, whereas milk samples collected prior to the COVID-19 pandemic were unable to do so Taken together, our data do not support mother-to-infant transmission of SARS-CoV-2 via milk Importantly, milk produced by infected mothers is a beneficial source of anti-SARS-CoV-2 IgA and IgG and neutralizes SARS-CoV-2 activity These results support recommendations to continue breastfeeding during mild-to-moderate maternal COVID-19 illness IMPORTANCE Results from prior studies assaying human milk for the presence of SARS-CoV-2, the causative virus of COVID-19, have suggested milk may act as a potential vehicle for mother-to-child transmission Most previous studies are limited because they followed only a few participants, were cross-sectional, and/or failed to report how milk was collected and/or analyzed As such, considerable uncertainty remains regarding whether human milk is capable of transmitting SARS-CoV-2 from mother to child Here, we report that repeated milk samples collected from 18 women following COVID-19 diagnosis did not contain SARS-CoV-2 RNA; however, risk of transmission via breast skin should be further evaluated Importantly, we found that milk produced by infected mothers is a source of anti-SARS-CoV-2 IgA and IgG and neutralizes SARS-CoV-2 activity These results support recommendations to continue breastfeeding during mild-to-moderate maternal COVID-19 illness as milk likely provides specific immunologic benefits to infants

Insights on forming N,O-coordinated Cu single-atom catalysts for electrochemical reduction CO2 to methane

Abstract: Single-atom catalysts (SACs) are promising candidates to catalyze electrochemical CO2 reduction (ECR) due to maximized atomic utilization. However, products are usually limited to CO instead of hydrocarbons or oxygenates due to unfavorable high energy barrier for further electron transfer on synthesized single atom catalytic sites. Here we report a novel partial-carbonization strategy to modify the electronic structures of center atoms on SACs for lowering the overall endothermic energy of key intermediates. A carbon-dots-based SAC margined with unique CuN2O2 sites was synthesized for the first time. The introduction of oxygen ligands brings remarkably high Faradaic efficiency (78%) and selectivity (99% of ECR products) for electrochemical converting CO2 to CH4 with current density of 40 mA·cm-2 in aqueous electrolytes, surpassing most reported SACs which stop at two-electron reduction. Theoretical calculations further revealed that the high selectivity and activity on CuN2O2 active sites are due to the proper elevated CH4 and H2 energy barrier and fine-tuned electronic structure of Cu active sites. Single-atom catalysts (SACs) are promising candidates to catalyze CO2 reduction for the formation of high value hydrocarbons but most of the reactions yield CO. Here, the authors show a low-temperature calcining process to fabricate a carbon-dots-based SAC to efficiently convert CO2 to methane.

Examining the Dimensionality, Reliability, and Invariance of the Depression, Anxiety, and Stress Scale–21 (DASS-21) Across Eight Countries:

Abstract: This study evaluated the dimensionality, invariance, and reliability of the Depression, Anxiety, and Stress Scale-21 (DASS-21) within and across Brazil, Canada, Hong Kong, Romania, Taiwan, Turkey, United Arab Emirates, and the United States (N = 2,580) in college student samples. We used confirmatory factor analyses to compare the fit of four different factor structures of the DASS-21: a unidimensional model, a three-correlated-factors model, a higher order model, and a bifactor model. The bifactor model, with three specific factors (depression, anxiety, and stress) and one general factor (general distress), presented the best fit within each country. We also calculated ancillary bifactor indices of model-based dimensionality of the DASS-21 and model-based reliability to further examine the validity of the composite total and subscale scores and the use of unidimensional modeling. Results suggested the DASS-21 can be used as a unidimensional scale. Finally, measurement invariance of the best fitting model was tested across countries indicating configural invariance. The traditional three-correlated-factors model presented scalar invariance across Canada, Hong Kong, Romania, Taiwan, and the United States. Overall, these analyses indicate that the DASS-21 would best be used as a general score of distress rather than three separate factors of depression, anxiety, and stress, in the countries studied.

Control of Agricultural Production Systems

Abstract: With the development and application of control theory and approach agricultural production systems should be implemented with improved performance. Precision management of agricultural production systems has been developed and applied since the 1980s, through the 2010s, to present with advanced digital agricultural information technologies. Agricultural cybernetics (AC) provides precision agricultural production management new insights into what the systems can do with information exchange and communication and how the systems are controlled with schemes designed with control theory and compared with the application in industrial environment to come up to a generic agricultural cybernetic system.

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Abstract: Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

Status and prospects of genome-wide association studies in plants.

Abstract: Genome-wide association studies (GWAS) have developed into a powerful and ubiquitous tool for the investigation of complex traits. In large part, this was fueled by advances in genomic technology, enabling us to examine genome-wide genetic variants across diverse genetic materials. The development of the mixed model framework for GWAS dramatically reduced the number of false positives compared with naive methods. Building on this foundation, many methods have since been developed to increase computational speed or improve statistical power in GWAS. These methods have allowed the detection of genomic variants associated with either traditional agronomic phenotypes or biochemical and molecular phenotypes. In turn, these associations enable applications in gene cloning and in accelerated crop breeding through marker assisted selection or genetic engineering. Current topics of investigation include rare-variant analysis, synthetic associations, optimizing the choice of GWAS model, and utilizing GWAS results to advance knowledge of biological processes. Ongoing research in these areas will facilitate further advances in GWAS methods and their applications.

Secondary Transition Predictors of Postschool Success: An Update to the Research Base:

Abstract: Research suggests youth with disabilities are less likely to experience positive outcomes compared to peers without disabilities. Identification of in-school predictors of postschool success can pr...

Biosensors based on fluorescence carbon nanomaterials for detection of pesticides

Abstract: Fluorescence carbon nanomaterials-based sensors for accurate tracing of pesticides in environmental, food and biological samples have gained considerable interest in the past decade years to protect ecosystem, guarantee food safety and prevent disease, making it a trending hot-spot. This review focuses on recent advances and new trends of pesticides monitoring (including organophosphorus, neonicotinoids and carbamates pesticides) on the base of fluorescence carbon nanomaterials, with particular emphasis on zero-dimensional (0-D) carbon dots/graphene quantum dots, 2-D carbon nitride nanosheets and 3-D carbon-based metal/covalent organic frameworks. These fluorometric strategies are classified by several main recognition unit, including enzyme, antibody, aptamer and molecularly-imprinted polymers, offering great performance for pesticides with a limit of detection down to pg mL−1 level. Beyond performance comparison of these emerging sensors with other strategies, we discuss the existing hurdles and present challenges to practical sensor designs, followed by exploring future perspectives for breakthroughs in fluorescence carbon nanomaterials-based sensors.

Single-atom catalysts boost signal amplification for biosensing.

Abstract: Development of highly sensitive biosensors has received ever-increasing attention over the years. Due to the unique physicochemical properties, the functional nanomaterial-enabled signal amplification strategy has made some great breakthroughs in biosensing. However, the sensitivity and selectivity still need further improvement. Single-atom catalysts (SACs) containing atomically dispersed metal active sites demonstrate distinctive advantages in catalytic activity and selectivity for various catalytic reactions. As a consequence, the SAC-enabled signal amplification strategy holds great promise in biosensors, demonstrating satisfactory sensitivity and selectivity with the assistance of tunable metal–support interactions, coordination environments and geometric/electronic structures of active sites. In this tutorial review, we briefly discuss the structural advantages of SACs. Then, the catalytic mechanism at the atomic scale and signal amplification effects of SACs in the colorimetric, electrochemical, chemiluminescence, electrochemiluminescence, and photoelectrochemical biosensing applications are highlighted in detail. Finally, opportunities and challenges to be faced in the future development of the SAC-enabled signal amplification strategy for biosensing are discussed and outlooked.

Representation and participation across 20 years of plant genome sequencing.

Abstract: The field of plant genome sequencing has grown rapidly in the past 20 years, leading to increases in the quantity and quality of publicly available genomic resources. The growing wealth of genomic data from an increasingly diverse set of taxa provides unprecedented potential to better understand the genome biology and evolution of land plants. Here we provide a contemporary view of land plant genomics, including analyses on assembly quality, taxonomic distribution of sequenced species and national participation. We show that assembly quality has increased dramatically in recent years, that substantial taxonomic gaps exist and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of study species. We identify numerous disconnects between the native range of focal species and the national affiliation of the researchers studying them, which we argue are rooted in colonialism-both past and present. Luckily, falling sequencing costs, widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps and empower a more global plant genomics community.