AKAP12 Upregulation Associates With PDE8A to Accelerate Cardiac Dysfunction.

BACKGROUND: In heart failure, signaling downstream the ß2-adrenergic receptor is critical. Sympathetic stimulation of ß2-adrenergic receptor alters cAMP (cyclic adenosine 3',5'-monophosphate) and triggers PKA (protein kinase A)-dependent phosphorylation of proteins that regulate cardiac function. cAMP levels are regulated in part by PDEs (phosphodiesterases). Several AKAPs (A kinase anchoring proteins) regulate cardiac function and are proposed as targets for precise pharmacology. AKAP12 is expressed in the heart and has been reported to directly bind ß2-adrenergic receptor, PKA, and PDE4D. However, its roles in cardiac function are unclear. METHODS: cAMP accumulation in real time downstream of the ß2-adrenergic receptor was detected for 60 minutes in live cells using the luciferase-based biosensor (GloSensor) in AC16 human-derived cardiomyocyte cell lines overexpressing AKAP12 versus controls. Cardiomyocyte intracellular calcium and contractility were studied in adult primary cardiomyocytes from male and female mice overexpressing cardiac AKAP12 (AKAP12OX) and wild-type littermates post acute treatment with 100-nM isoproterenol (ISO). Systolic cardiac function was assessed in mice after 14 days of subcutaneous ISO administration (60 mg/kg per day). AKAP12 gene and protein expression levels were evaluated in left ventricular samples from patients with end-stage heart failure. RESULTS: AKAP12 upregulation significantly reduced total intracellular cAMP levels in AC16 cells through PDE8. Adult primary cardiomyocytes from AKAP12OX mice had significantly reduced contractility and impaired calcium handling in response to ISO, which was reversed in the presence of the selective PDE8 inhibitor (PF-04957325). AKAP12OX mice had deteriorated systolic cardiac function and enlarged left ventricles. Patients with end-stage heart failure had upregulated gene and protein levels of AKAP12. CONCLUSIONS: AKAP12 upregulation in cardiac tissue is associated with accelerated cardiac dysfunction through the AKAP12-PDE8 axis.

Naturally occurring substitution of an amino acid in a plant virus gene-silencing suppressor enhances viral adaptation to increasing thermal stress.

Cereal yellow dwarf virus (CYDV-RPV) encodes a P0 protein that functions as a viral suppressor of RNA silencing (VSR). The strength of silencing suppression is highly variable among CYDV-RPV isolates. In this study, comparison of the P0 sequences of CYDV-RPV isolates and mutational analysis identified a single C-terminal amino acid that influenced P0 RNA-silencing suppressor activity. A serine at position 247 was associated with strong suppressor activity, whereas a proline at position 247 was associated with weak suppressor activity. Amino acid changes at position 247 did not affect the interaction of P0 with SKP1 proteins from Hordeum vulgare (barley) or Nicotiana benthamiana. Subsequent studies found P0 proteins containing a P247 residue were less stable than the P0 proteins containing an S247 residue. Higher temperatures contributed to the lower stability and in planta and the P247 P0 proteins were subject to degradation via the autophagy-mediated pathway. A P247S amino acid residue substitution in P0 increased CYDV-RPV replication after expression in agroinfiltrated plant leaves and increased viral pathogenicity of P0 generated from the heterologous Potato virus X expression vector system. Moreover, an S247 CYDV-RPV could outcompete the P247 CYDV-RPV in a mixed infection in natural host at higher temperature. These traits contributed to increased transmission by aphid vectors and could play a significant role in virus competition in warming climates. Our findings underscore the capacity of a plant RNA virus to adapt to climate warming through minor genetic changes in gene-silencing suppressor, resulting in the potential for disease persistence and prevalence.

Ecological structure of diversity-dependent diversification in Phanerozoic marine bivalves.

Rigorous analysis of diversity-dependence-the hypothesis that the rate of proliferation of new species is inversely related to standing diversity-requires consideration of the ecology of the organisms in question. Differences between infaunal marine bivalves (living entirely within the sediment) and epifaunal forms (living partially or completely above the sediment-water interface) predict that these major ecological groups should have different diversity dynamics: epifaunal species may compete more intensely for space and be more susceptible to predation and physical disturbance. By comparing detrended standing diversity with rates of diversification, origination, and extinction in this exceptional fossil record, we find that epifaunal bivalves experienced significant, negative diversity-dependence in origination and net diversification, whereas infaunal forms show little appreciable relationship between diversity and evolutionary rates. This macroevolutionary contrast is robust to the time span over which dynamics are analysed, whether mass-extinction rebounds are included in the analysis, the treatment of stratigraphic ranges that are not maximally resolved, and the details of detrending. We also find that diversity-dependence persists over hundreds of millions of years, even though diversity itself rises nearly exponentially, belying the notion that diversity-dependence must imply equilibrial diversity dynamics.

Convergence and contingency in the evolution of a specialized mode of life: multiple origins and high disparity of rock-boring bivalves.

Evolutionary adaptation to novel, specialized modes of life is often associated with a close mapping of form to the new function, resulting in narrow morphological disparity. For bivalve molluscs, endolithy (rock-boring) has biomechanical requirements thought to diverge strongly from those of ancestral functions. However, endolithy in bivalves has originated at least eight times. Three-dimensional morphometric data representing 75 species from approximately 94% of extant endolithic genera and families, along with 310 non-endolithic species in those families, show that endolithy is evolutionarily accessible from many different morphological starting points. Although some endoliths appear to converge on certain shell morphologies, the range of endolith shell form is as broad as that belonging to any other bivalve substrate use. Nevertheless, endolithy is a taxon-poor function in Bivalvia today. This limited richness does not derive from origination within source clades having significantly low origination or high extinction rates, and today's endoliths are not confined to low-diversity biogeographic regions. Instead, endolithy may be limited by habitat availability. Both determinism (as reflected by convergence among distantly related taxa) and contingency (as reflected by the endoliths that remain close to the disparate morphologies of their source clades) underlie the occupation of endolith morphospace.

Aortocoronary dissection during percutaneous coronary interventions for chronic total occlusion: Insights from the PROGRESS-CTO registry.

BACKGROUND: Aortocoronary dissection is a potentially serious complication of chronic total occlusion (CTO) percutaneous coronary intervention (PCI). METHODS: We examined the incidence, mechanisms, treatment, and outcomes of aortocoronary dissection among 12,117 CTO PCIs performed between 2012 and 2022 in a large multicenter CTO PCI registry. RESULTS: The incidence of aortocoronary dissection was 0.2% (n = 27). Most aortocoronary dissections occurred in the right coronary artery (96.3%, n = 26). The baseline clinical characteristics of patients with and without aortocoronary dissection were similar, except for dyslipidemia, which was less common in patients with aortocoronary dissection (70.4% vs. 86.0%; p = 0.019). The retrograde approach was used more commonly among cases complicated by aortocoronary dissection (59.3% vs. 31.0%; p = 0.002). Technical (74.1% vs. 86.6%; p = 0.049) and procedural (70.4% vs. 85.2%; p = 0.031) success rates were lower among aortocoronary dissection cases, with a similar incidence of in-hospital major adverse cardiovascular events (3.7% vs. 2.0%; p = 0.541). Of the 27 patients with aortocoronary dissection, 19 (70.4%) were treated with ostial stenting and 8 (29.6%) were treated conservatively without subsequent adverse clinical outcomes. No patients required emergency surgery. Follow-up was available for 22 patients (81.5%): during a mean follow up of 767 (±562) days, the incidence of in-stent restenosis was 11.1% (n = 3). CONCLUSIONS: Aortocoronary dissection occurred in 0.2% of CTO PCIs performed by experienced operators, was associated with lower technical and procedural success, and was treated most commonly with ostial stenting. None of the patients required emergency cardiac surgery.

Incidence, mechanisms, treatment, and outcomes of donor vessel injury during percutaneous coronary interventions for chronic total occlusion.

BACKGROUND: Donor vessel injury is a potentially life-threatening complication of chronic total occlusion (CTO) percutaneous coronary intervention (PCI). AIMS: Our goal was to examine the incidence, mechanisms, treatment, and outcomes of patients with donor vessel injury in a large multicenter CTO PCI registry. METHODS: We analyzed the baseline clinical and angiographic characteristics, and procedural outcomes of 12,349 CTO PCIs performed between 2012 and 2022 at 44 centers. RESULTS: The incidence of donor vessel injury was 0.35% (n = 43). The baseline clinical characteristics of patients with and without donor vessel injury were similar. Cases complicated by donor vessel injury were more complex with higher Japanese CTO score (2.9 ± 1.1 vs. 2.4 ± 1.3; p = 0.004) and lower procedural success rate (69.8% vs. 85.2%; p = 0.004). The retrograde approach was used more commonly in donor vessel injury cases (68.9% vs. 30.9%; p < 0.001). Most (53.5%) donor vessel injuries were guide catheter-induced, whereas 20.9% were due to donor vessel thrombosis. Of the 43 patients with donor vessel injury, 36 (83.7%) were treated with stenting and seven (16.3%) received a left ventricular assist device. The incidence of major adverse cardiovascular events (MACEs) was significantly higher in cases with donor vessel injury (23.3% vs. 2.0%; p < 0.001). Of the 43 patients with donor vessel injury, five patients (11.6%) experienced acute myocardial infarction and four patients (9.3%) died. CONCLUSIONS: Donor vessel injury, occurred in 0.35% of CTO PCIs performed by experienced operators, was mainly due to guide catheter-induced dissection or thrombosis and was associated with lower procedural success and higher MACE.

Trends in botanical exploration in Nigeria forecast over 1000 yet undescribed vascular plant species.

BACKGROUND AND AIMS: Taxonomists are primary actors of biodiversity assessment. At the same time, there is awareness by the taxonomic community at large that the field is going through a crisis, sometimes referred to as the "taxonomic impediment". Coupled with the ongoing biodiversity crisis, or 6 th mass extinction, this biodiversity impedance puts at risk the target set in the Convention on Biological Diversity's Global Biodiversity Framework vision 2050, which calls for urgent action to "…put biodiversity on a path to recovery by 2030 for the benefit of planet and people". This risk is particularly pronounced in tropical African countries where taxonomic studies are done on an ad hoc basis. In this study, our aim is to investigate the historical trends in botanical exploration of vascular plants in Nigeria and forecast the near-term (50 year) description of presently unknown species, which we use to discuss scenarios of taxonomic effort that may be necessary for a comprehensive biodiversity assessment in the country. METHODS: The study is based on a dataset from the World Checklist of Vascular Plants (WCVP), containing all vascular plant species reported to occur in Nigeria. We fit nested Bayesian time series regressions to estimate the long-term trend in the rate of description of vascular plant species in Nigeria. From these models, we use an ensemble forecast to estimate the number of species descriptions by the year 2070, and then evaluate the description rates per taxonomist required to meet this estimate under different totals of active taxonomists. KEY RESULTS: We find a striking difference in species description between Nigerian botanists and their foreign counterparts, with the former contributing relatively small numbers. Additionally, only a fraction of the authors involved in describing Nigeria's vascular plants are of indigenous origin. Our study reveals that the number of new species described annually exhibits a long-term increasing trend, with an average of 19.5 species described per year. However, after taking into account year-to-year variability and the number of taxonomists active in a given year, the long-term trend in species descriptions credibly declines over time. While the number of authors involved in describing species has generally increased over time, it remained stable since the 1950s. Predictions for the number of new species descriptions by 2070 vary by model, with an ensemble prediction estimating 1140 species descriptions, but ranging from 1004 to 2239 between individual models. CONCLUSIONS: The study estimates that current levels of taxonomic activity should lead to a 20% increase in known species of vascular plants in Nigeria over the next 50 years, which is still likely an underestimate of the true, unknown species richness. Urgent action is needed to address the taxonomic impediment so that local taxonomic studies in tropical African countries can achieve the CBD's Global Biodiversity Framework vision 2050. Here, we outline some key pathways to achieving this goal.

Cambrian origin but no early burst in functional disparity for Class Bivalvia.

Both the Cambrian explosion, more than half a billion years ago, and its Ordovician aftermath some 35 Myr later, are often framed as episodes of widespread ecological opportunity, but not all clades originating during this interval showed prolific rises in morphological or functional disparity. In a direct analysis of functional disparity, instead of the more commonly used proxy of morphological disparity, we find that ecological functions of Class Bivalvia arose concordantly with and even lagged behind taxonomic diversification, rather than the early-burst pattern expected for clades originating in supposedly open ecological landscapes. Unlike several other clades originating in the Cambrian explosion, the bivalves' belated acquisition of key anatomical novelties imposed a macroevolutionary lag, and even when those novelties evolved in the Early Ordovician, functional disparity never surpassed taxonomic diversity. Beyond this early period of animal evolution, the founding and subsequent diversification of new major clades and their functions might be expected to follow the pattern of the early bivalves-one where interactions between highly dynamic environmental and biotic landscapes and evolutionary contingencies need not promote prolific functional innovation.

Four-year review of New Zealand laboratory infliximab and adalimumab concentration results indicating potential for improved dosing.

A review of laboratory results across New Zealand for therapeutic drug monitoring (TDM) of infliximab and adalimumab concentrations and antidrug antibodies (ADAs) over 4 years was completed. Of 6591 results, the median serum concentration for infliximab was 5.7 mg/L and for adalimumab was 5.5 mg/L. Subtherapeutic drug concentrations (<7 mg/L) were measured in 54% of samples. Drug concentrations <2 mg/L were measured in 23% of samples, with ADAs detected in 51% of these. The high number of samples with subtherapeutic drug concentrations and common ADA detection is consistent with failing therapy but could also suggest that standard dosing is frequently too low for patients. These results reinforce the value of antitumour necrosis factor drug TDM in making decisions to adjust dosing or switch agents in patients taking infliximab and adalimumab.

Efficacy of detergent-based cleaning and wiping against SARS-CoV-2 on high-touch surfaces.

Efficacy of cleaning methods against SARS-CoV-2 suspended in either 5% soil load (SARS-soil) or simulated saliva (SARS-SS) was evaluated immediately (hydrated virus, T0) or 2 hours post-contamination (dried virus, T2). Hard water dampened wiping (DW) of surfaces, resulted in 1.77-3.91 log reduction (T0) or 0.93-2.41 log reduction (T2). Incorporating surface pre-wetting by spraying with a detergent solution (D + DW) or hard water (W + DW) just prior to dampened wiping did not unilaterally increase efficacy against infectious SARS-CoV-2, however, the effect was nuanced with respect to surface, viral matrix, and time. Cleaning efficacy on porous surfaces (seat fabric, SF) was low. W + DW on stainless steel (SS) was as effective as D + DW for all conditions except SARS-soil at T2 on SS. DW was the only method that consistently resulted in > 3-log reduction of hydrated (T0) SARS-CoV-2 on SS and ABS plastic. These results suggest that wiping with a hard water dampened wipe can reduce infectious virus on hard non-porous surfaces. Pre-wetting surfaces with surfactants did not significantly increase efficacy for the conditions tested. Surface material, presence or absence of pre-wetting, and time post-contamination affect efficacy of cleaning methods.

Infection Dynamics of Potato Virus Y Isolate Combinations in Three Potato Cultivars.

The United States potato industry has recently experienced a strain shift; recombinant potato virus Y (PVY) strains (e.g., PVYNTN) have emerged as the predominant strains over the long dominant ordinary strain (PVYO), yet both are often found as single infections within the same field and as mixed infections within individual plants. To understand mixed infection dynamics in potato plants and in daughter tubers, three potato varieties varying for PVY resistance, 'Red Maria', 'CalWhite', and 'Pike', were mechanically inoculated either at the pre- or postflowering stage with all possible heterologous isolate combinations of two PVYO and two PVYNTN isolates. Virus titer was determined from leaves collected at different positions on the plant at different times, and tuber-borne infection was determined for two successive generations. PVYNTN accumulated to higher levels than PVYO at nearly all sampling time points in 'Pike' potato. However, both virus strains accumulated to similar amounts in 'Red Maria' and 'CalWhite' potato early in the infection when inoculated preflowering; however, PVYNTN dominated at later stages and in plants inoculated postflowering. Regardless of inoculation time, both virus strains were transmitted to daughter plants raised from the tubers for most isolate combinations. The relative titer of PVYNTN and PVYO isolates at the later stages of mother plant development was indicative of what was found in the daughter plants. Although virus titer differed among cultivars depending on their genetics and virus isolates, it did not change the strain outcome in tuber-borne infection in subsequent generations. Differential virus accumulation in these cultivars suggests isolate-specific resistance to PVY accumulation.

Evolutionary modularity, integration and disparity in an accretionary skeleton: analysis of venerid Bivalvia.

Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channelling morphological evolution along lines of least resistance-a process that may be particularly important in the accumulation of disparity in the many invertebrate systems having accretionary growth. We use a time-calibrated phylogenetic hypothesis and high-density, three-dimensional semilandmarking to analyse the relationship between modularity, integration and disparity in the most diverse extant bivalve family: the Veneridae. In general, venerids have a simple, two-module parcellation of their body that is divided into features of the calcium carbonate shell and features of the internal soft anatomy. This division falls more along developmental than functional lines when placed in the context of bivalve anatomy and biomechanics. The venerid body is tightly integrated in absolute terms, but disparity appears to increase with modularity strength among subclades and ecologies. Thus, shifts towards more mosaic evolution beget higher morphological variance in this speciose family.

Gender differences in chronic total occlusion percutaneous coronary interventions: Insights from the PROGRESS-CTO registry.

BACKGROUND: There are limited data describing gender differences in patients undergoing chronic total occlusion (CTO) percutaneous coronary interventions (PCI). METHODS: We compared baseline clinical and angiographic characteristics and procedural outcomes between men and women among 9457 CTO PCIs performed at 38 centers between 2012 and 2022. RESULTS: A total of 7687 (81%) men and 1770 (19%) women were treated. Women were older, more likely to have comorbidities such as diabetes, hypertension and peripheral arterial disease, and had higher left ventricular ejection fraction. The most common CTO target vessel was the right coronary artery for both men (53%) and women (52%), although the left anterior descending artery was more frequently the target vessel among women (31% vs. 25%; p < 0.001). The J-CTO score (2.4 ± 1.3 vs. 2.2 ± 1.2; p < 0.001) as well as the PROGRESS-CTO score (1.3 ± 1.0 vs. 1.1 ± 1.0; p < 0.001) were higher among men. In female patients, antegrade wiring was more frequently the initial crossing strategy (87.6% vs. 82.4%; p < 0.001) and was more successful in crossing the target lesion (62.7% vs. 54.0%; p < 0.001) compared with men. Interventions in men required longer procedure time and fluoroscopy time, as well as higher air kerma radiation dose and contrast volume when compared to women. Technical (89% vs. 86%; p < 0.001) and procedural (87% vs. 84%; p = 0.003) success rates were higher among women. In-hospital major adverse cardiovascular events (MACE) were also higher in women (2.9% vs. 1.8%; p < 0.001). CONCLUSIONS: Women undergoing CTO PCI had higher technical and procedural success rates, but also higher in-hospital MACE compared with men.

Knowledge and Attitudes of Potential Community Health Worker Employers: Findings from the State of Arkansas, USA.

Community health workers (CHWs) are critical to health equity efforts, but sustaining CHW programs is challenging. Understanding stakeholders' knowledge and attitudes about CHWs can inform strategies to advance this important workforce. The authors implemented an online survey of potential CHW employers to learn their perceptions of CHWs' roles, outcomes, and abilities to affect important health outcomes, and of key issues that affect CHW employment. The survey was disseminated statewide to a diverse group of stakeholders working in healthcare in Arkansas. A total of 151 surveys were collected and included in the analysis. The organizations represented by respondents primarily included state and local agencies and clinics, followed by healthcare systems. The main professional roles of survey respondents were administrators and clinicians, followed by healthcare staff. Over 90% of respondents agreed that CHWs have the ability to conduct community outreach, serve as a liaison, navigate health systems, provide coaching support, and participate in care coordination. Over 90% of healthcare administrators, clinicians, and policymakers agreed that standardized training and a clear definition of role and scope of practice are important to CHW employment. However, almost two-thirds of respondents' organizations were not employing CHWs, adding to previous research which has primarily focused on CHW employers' attitudes. Understanding and addressing attitudes of those who lack experience with CHWs can help to identify actions needed to promote and increase adoption of CHWs. The authors share how they are using these data to engage stakeholders in decision-making and adoption of CHWs in their state.

Effects of provision of drinking water on the behavior and growth rate of group-housed calves with different milk allowances.

Despite the clear importance of drinking water, calves are not always provided water on farm for the first few weeks of life. The main objective of this study was to investigate the effects of water provision (access or no access) and milk allowance (high or low) on the behavior and growth rate of calves. Fifty mixed-breed calves were each assigned to 1 of 4 treatments: (1) water and high (10 L/d) milk allowance (n = 13), (2) no water and high milk allowance (n = 12), (3) water and low (5 L/d) milk allowance (n = 12), or (4) no water and low milk allowance (n = 13). Visits to the water trough, water intake, milk drinking behavior (visits and drinking speed), proportion of observations eating hay and calf starter, and lying behavior were recorded from when the calves were, on average, 5 d of age (standard deviation: 2 d) for 4 consecutive weeks. Calves were weighed weekly. Some calves began to visit the water trough from the start of the recording period, as early as 4 d of age, and water intake increased with age for all calves that had access to it. This increase was greater for calves provided a high milk allowance. Water intake increased with ambient temperature, which highlights the importance of providing drinking water in warm conditions. Overall, calves spent a greater proportion of observations eating hay and calf starter with age. The provision of drinking water was associated with a greater proportion of observations eating hay but less eating calf starter. The increase in the proportion of observations eating calf starter with age was greater for calves on a low milk allowance than of those provided a high milk allowance; this is likely due to calves on a low milk allowance searching for nutrients and energy. Calves on a high milk allowance grew faster and spent more time lying compared with calves with a low milk allowance, thus suggesting greater satiety of well-fed calves. Our results suggest that calves should have free access to drinking water from birth and that access to drinking water may aid in hay (fiber) intake and possibly rumen development.

Evaluation of surface disinfection methods to inactivate the beta coronavirus Murine Hepatitis Virus.

The list of EPA-approved disinfectants for coronavirus features many products for use on hard, non-porous materials. There are significantly fewer products registered for use on porous materials. Further, many common, high-touch surfaces fall in between non-porous materials such as glass and porous materials such as soft fabrics. The objective of this study was to assess the efficacy of selected commercially available disinfectant products against coronaviruses on common, high-touch surfaces. Four disinfectants (Clorox Total 360, Bleach solution, Vital Oxide, and Peroxide Multi-Surface Cleaner) were evaluated against Murine Hepatitis Virus A59 (MHV) as a surrogate coronavirus for SARS-CoV-2. MHV in cell culture medium was inoculated onto four materials: stainless steel, latex-painted drywall tape, Styrene Butadiene rubber (rubber), and bus seat fabric. Immediately (T0) or 2-hr (T2) post-inoculation, disinfectants were applied by trigger-pull or electrostatic sprayer and either held for recommended contact times (Spray only) or immediately wiped (Spray and Wipe). Recovered infectious MHV was quantified by median tissue culture infectious dose assay. Bleach solution, Clorox Total 360, and Vital Oxide were all effective (>3-log10 reduction or complete kill of infectious virus) with both the Spray Only and Spray and Wipe methods on stainless steel, rubber, and painted drywall tape when used at recommended contact times at both T0 and T2 hr. Multi-Surface Cleaner unexpectedly showed limited efficacy against MHV on stainless steel within the recommended contact time; however, it showed increased (2.3 times greater efficacy) when used in the Spray and Wipe method compared to Spray Only. The only products to achieve a 3-log10 reduction on fabric were Vital Oxide and Clorox Total 360; however, the efficacy of Vital Oxide against MHV on fabric was reduced to below 3-log10 when applied by an electrostatic sprayer compared to a trigger-pull sprayer. This study highlights the importance of considering the material, product, and application method when developing a disinfection strategy for coronaviruses on high-touch surfaces.

Affinity Purification-Mass Spectrometry Identifies a Novel Interaction between a Polerovirus and a Conserved Innate Immunity Aphid Protein that Regulates Transmission Efficiency.

The vast majority of plant viruses are transmitted by insect vectors, with many crucial aspects of the transmission process being mediated by key protein-protein interactions. Still, very few vector proteins interacting with viruses have been identified and functionally characterized. Potato leafroll virus (PLRV) is transmitted most efficiently by Myzus persicae, the green peach aphid, in a circulative, non-propagative manner. Using affinity purification coupled to high-resolution mass spectrometry (AP-MS), we identified 11 proteins from M. persicaedisplaying a high probability of interaction with PLRV and an additional 23 vector proteins with medium confidence interaction scores. Three of these aphid proteins were confirmed to directly interact with the structural proteins of PLRV and other luteovirid species via yeast two-hybrid. Immunolocalization of one of these direct PLRV-interacting proteins, an orthologue of the human innate immunity protein complement component 1 Q subcomponent-binding protein (C1QBP), shows that MpC1QBP partially co-localizes with PLRV in cytoplasmic puncta and along the periphery of aphid gut epithelial cells. Artificial diet delivery to aphids of a chemical inhibitor of C1QBP leads to increased PLRV acquisition by aphids and subsequently increased titer in inoculated plants, supporting a role for C1QBP in the acquisition and transmission efficiency of PLRV by M. persicae. This study presents the first use of AP-MS for the in vivo isolation of a functionally relevant insect vector-virus protein complex. MS data are available from ProteomeXchange.org using the project identifier PXD022167.

Virus and helper component interactions favour the transmission of recombinant potato virus Y strains.

In recent years, several recombinant strains of potato virus Y, notably PVYNTN and PVYN:O have displaced the ordinary strain, PVYO, and emerged as the predominant strains affecting the USA potato crop. Previously we reported that recombinant strains were transmitted more efficiently than PVYO when they were acquired sequentially, regardless of acquisition order. In another recent study, we showed that PVYNTN binds preferentially to the aphid stylet over PVYO when aphids feed on a mixture of PVYO and PVYNTN. To understand the mechanism of this transmission bias as well as preferential virus binding, we separated virus and active helper component proteins (HC), mixed them in homologous and heterologous combinations, and then fed them to aphids using Parafilm sachets. Mixtures of PVYO HC with either PVYN:O or PVYNTN resulted in efficient transmission. PVYN:O HC also facilitated the transmission of PVYO and PVYNTN, albeit with reduced efficiency. PVYNTN HC failed to facilitate transmission of either PVYO or PVYN:O. When PVYO HC or PVYN:O HC was mixed with equal amounts of the two viruses, both viruses in all combinations were transmitted at high efficiencies. In contrast, no transmission occurred when combinations of viruses were mixed with PVYNTN HC. Further study evaluated transmission using serial dilutions of purified virus mixed with HCs. While PVYNTN HC only facilitated the transmission of the homologous virus, the HCs of PVYO and PVYN:O facilitated the transmission of all strains tested. This phenomenon has likely contributed to the increase in the recombinant strains affecting the USA potato crop.

Different potato virus Y strains frequently co-localize in single epidermal leaf cells and in the aphid stylet.

Single aphids can simultaneously or sequentially acquire and transmit multiple potato virus Y (PVY) strains. Multiple PVY strains are often found in the same field and occasionally within the same plant, but little is known about how PVY strains interact in plants or in aphid stylets. Immuno-staining and confocal microscopy were used to examine the spatial and temporal dynamics of PVY strain mixtures (PVYO and PVYNTN or PVYO and PVYN) in epidermal leaf cells of 'Samsun NN' tobacco and 'Goldrush' potato. Virus binding and localization was also examined in aphid stylets following acquisition. Both strains systemically infected tobacco and co-localized in cells of all leaves examined; however, the relative amounts of each virus changed over time. Early in the tobacco infection, when mosaic symptoms were observed, PVYO dominated the infection although PVYNTN was detected in some cells. As the infection progressed and vein necrosis developed, PVYNTN was prevalent. Co-localization of PVYO and PVYN was also observed in epidermal cells of potato leaves with most cells infected with both viruses. Furthermore, two strains could be detected binding to the distal end of aphid stylets following virus acquisition from a plant infected with a strain mixture. These data are in contrast with the traditional belief of spatial separation of two closely related potyviruses and suggest apparent non-antagonistic interaction between PVY strains that could help explain the multitude of emerging recombinant PVY strains discovered in potato in recent years.

Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project.

BACKGROUND: Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy; however, there is empirical variability across panel assays and factors contributing to this variability have not been comprehensively investigated. Identifying sources of variability can help facilitate comparability across different panel assays, which may aid in broader adoption of panel assays and development of clinical applications. MATERIALS AND METHODS: Twenty-nine tumor samples and 10 human-derived cell lines were processed and distributed to 16 laboratories; each used their own bioinformatics pipelines to calculate TMB and compare to whole exome results. Additionally, theoretical positive percent agreement (PPA) and negative percent agreement (NPA) of TMB were estimated. The impact of filtering pathogenic and germline variants on TMB estimates was assessed. Calibration curves specific to each panel assay were developed to facilitate translation of panel TMB values to whole exome sequencing (WES) TMB values. RESULTS: Panel sizes >667 Kb are necessary to maintain adequate PPA and NPA for calling TMB high versus TMB low across the range of cut-offs used in practice. Failure to filter out pathogenic variants when estimating panel TMB resulted in overestimating TMB relative to WES for all assays. Filtering out potential germline variants at >0% population minor allele frequency resulted in the strongest correlation to WES TMB. Application of a calibration approach derived from The Cancer Genome Atlas data, tailored to each panel assay, reduced the spread of panel TMB values around the WES TMB as reflected in lower root mean squared error (RMSE) for 26/29 (90%) of the clinical samples. CONCLUSIONS: Estimation of TMB varies across different panels, with panel size, gene content, and bioinformatics pipelines contributing to empirical variability. Statistical calibration can achieve more consistent results across panels and allows for comparison of TMB values across various panel assays. To promote reproducibility and comparability across assays, a software tool was developed and made publicly available.