Analysis of two hypervariable human cytomegalovirus genes, UL146 and UL139

Abstract Human cytomegalovirus (HCMV) is a highly host-specific, ubiquitous herpesvirus that results in asymptomatic infection for the majority of those infected. However, it produces serious clinical disease in neonates and immunocompromised individuals such as transplant recipients and AIDS patients. The majority of the 236 kbp genome is highly conserved, but there are a number of highly variable regions, coding and non-coding, scattered throughout the genome. Numerous studies have been published investigating the genotypes of hypervariable genes, most focussed on potential associations between genotype and clinical disease or tropism. In general, no convincing connections between genotype and disease have been found. The present study investigated two hypervariable HCMV genes, UL146 and UL139, in a large number of clinical samples (179) from a number of locations worldwide in Europe, Africa, Asia and Australia. A total of 14 UL146 genotypes (G1-G14) were detected, which agrees with previous findings based on many fewer samples. For UL139, eight genotypes were detected, three of them (G5, G7 and G8) novel. The genotypes of both genes appear to have evolved under constraint rather than positive selection. Possible bias in the geographical distribution of the UL146 and UL139 genotypes was investigated. In general, all genotypes were found in all areas and any variation from the expected distribution was probably a result of small sample numbers from certain regions, specifically Asia and Australia. This general finding is in agreement with that of a previously published study on gene UL73. No evidence for linkage disequilibrium between UL146 and UL139 genotypes was found. This is in accordance with a previously published study of linkage disequilibrium among six other genes (UL55, UL74, UL75, UL115, US9 and US28), and is consistent with the theory that recombination has played a role in HCMV evolution. The absence of linkage between highly variable genes complicates attempts to examine associations between genotype and disease, as many combinations of genotypes are possible. Investigation of transcriptional expression of UL146 and UL139 from HCMV strain Merlin in fibroblast cell culture revealed that UL146 is expressed with late kinetics and UL139 with early-late kinetics. Northern blot and RACE data suggested that UL146 is 3’-coterminally expressed with UL147, UL147A, UL148 and UL132, and that UL139 is 3’-coterminally expressed with UL140 and UL141. To determine whether the high degree of sequence divergence corresponds to structural divergence, the UL146 genotypes were homology modelled on the related human chemokines IL-8, gro-a and IF9S. All 14 genotypes were predicted to be structurally very similar, which suggests they may also be functionally similar. However, small differences between the structures of human chemokines are known to result in slightly differing binding affinities for cellular receptors, and therefore even small differences between UL146 genotypes could conceivably confer functional differences. UL139 has been predicted to encode a type 1 membrane glycoprotein. No information has been published regarding UL139 function, although a short region of similarity with the cellular signal transducer CD24 has been noted previously, tentatively suggesting an immunomodulatory role. Preliminary experiments to characterise UL139 were performed utilising recombinant adenovirus vectors expressing tagged UL139 variants from three genotypes (G1, G5 and G7). The tagged UL139 variants expressed proteins that were considerably larger in mass than predicted from amino acid sequences. This extra mass may be attributable to glycosylation as well as other forms of post translational modification. Mixed infections of HCMV strains in immunocompromised individuals, such as transplant recipients, have been associated with enhanced pathogenesis and increased risk of transplant rejection. The presence of mixed infections also further complicates attempts to establish connections between genotype and disease outcome. In the analysis of UL146 and UL139 genotypes, multiple genotypes were detected in 14% of samples and in 29% when repeated experimental results were included, and even these values may be underestimations. The utility of a QPCR-based assay using genotype-specific primers was assessed as a means of more accurately determining the occurrence of mixed infections, and showed promise. Passage of HCMV strains in cell culture has been shown to result in various mutations. AD169, a commonly used laboratory strain, lacks 15 kbp sequence that includes UL146 and UL139. An alternative stock of AD169 (AD169varUC) was obtained that was thought to contain most or all of the deleted region and, indeed, both UL146 and UL139 were detected. Further sequencing confirmed that this stock is derived from AD169 and revealed that it contains all but 3.2 kbp of the 15 kbp absent from commonly used AD169 stocks. The 3.2 kbp deletion affects UL144, UL142, UL141 and UL140. This propensity of HCMV to undergo mutation during cell culture highlights the importance of studying characterised strains that are as close to wild type virus as possible

The Relationship between Cognition, Preseason Hitting Assessments, and In-Game Batting Performance in Collegiate Baseball and Softball Players

International Journal of Exercise Science 16(6): 23-30, 2023. Successful hitting performance may be related to perceptual processing of visual information. The purpose of this investigation was to examine the relationship between preseason cognitive assessments, off-field preseason hitting assessment, and in-game batting performing in collegiate baseball and softball athletes. Collegiate varsity baseball (n = 10, 20.5 ± 1.0 years) and softball (n = 16, 20.3 ± 1.3 years) underwent Flanker Task and Trail Maker Tests A (TMT-A) and B (TMT-B) 24 hours prior to a pre-seasoning indoor hitting assessment. During pre-season hitting assessment, athletes selected 10 underhand pitches and were outfitted with commercially available measurement tools (i.e., HitTrax and The Blast) to quantify swing characteristics. Batting average (BA), slugging percentage (SLUG) and on-base percentage (OBP) was obtained from subsequent 14 non-conference baseball and softball games. The data from this study demonstrated a relationship between the ball\u27s exit velocity (r = .501), bat velocity (r = .524) and average distance traveled (r = .449) during the hitting assessment and in-game BA, p \u3c 0.05. No relationship between hitting assessment outcomes and OBP or SLUG were detected, p \u3e 0.05. Furthermore, the Flanker-Task, TMT-A and TMT-B were not related to in game batting outcomes, p \u3e 0.05. Therefore, these data suggest that off-season preparation should be designed to maximize swing velocity while maintaining performance (i.e., skill) of the coordinated swing

Defining the content and delivery of an intervention to Change AdhereNce to treatment in BonchiEctasis (CAN-BE): a qualitative approach incorporating the Theoretical Domains Framework, behavioural change techniques and stakeholder expert panels

BackgroundLow patient adherence to treatment is associated with poorer health outcomes in bronchiectasis. We sought to use the Theoretical Domains Framework (TDF) (a framework derived from 33 psychological theories) and behavioural change techniques (BCTs) to define the content of an intervention to change patients’ adherence in bronchiectasis (Stage 1 and 2) and stakeholder expert panels to define its delivery (Stage 3).MethodsWe conducted semi-structured interviews with patients with bronchiectasis about barriers and motivators to adherence to treatment and focus groups or interviews with bronchiectasis healthcare professionals (HCPs) about their ability to change patients’ adherence to treatment. We coded these data to the 12 domain TDF to identify relevant domains for patients and HCPs (Stage 1). Three researchers independently mapped relevant domains for patients and HCPs to a list of 35 BCTs to identify two lists (patient and HCP) of potential BCTs for inclusion (Stage 2). We presented these lists to three expert panels (two with patients and one with HCPs/academics from across the UK). We asked panels who the intervention should target, who should deliver it, at what intensity, in what format and setting, and using which outcome measures (Stage 3).ResultsEight TDF domains were perceived to influence patients’ and HCPs’ behaviours: Knowledge, Skills, Beliefs about capability, Beliefs about consequences, Motivation, Social influences, Behavioural regulation and Nature of behaviours (Stage 1). Twelve BCTs common to patients and HCPs were included in the intervention: Monitoring, Self-monitoring, Feedback, Action planning, Problem solving, Persuasive communication, Goal/target specified:behaviour/outcome, Information regarding behaviour/outcome, Role play, Social support and Cognitive restructuring (Stage 2). Participants thought that an individualised combination of these BCTs should be delivered to all patients, by a member of staff, over several one-to-one and/or group visits in secondary care. Efficacy should be measured using pulmonary exacerbations, hospital admissions and quality of life (Stage 3).ConclusionsTwelve BCTs form the intervention content. An individualised selection from these 12 BCTs will be delivered to all patients over several face-to-face visits in secondary care. Future research should focus on developing physical materials to aid delivery of the intervention prior to feasibility and pilot testing. If effective, this intervention may improve adherence and health outcomes for those with bronchiectasis in the future

Nonmetropolitan Nebraskans’ Opinions about Water, Climate, and Energy: 2022 Nebraska Rural Poll Results

Most rural Nebraskans receive their home tap water from city water or municipal water systems. Just over two-thirds of rural Nebraskans receive their drinking water from a municipal system. One-quarter have private well water and seven percent are on a rural water system. Many rural Nebraskans have tested their home tap water for nitrates. However, a similar proportion indicated they have not tested their water or are unsure. Persons with higher household incomes are more likely than persons with lower incomes to have tested their home water for each of the items listed. Many persons with the lowest household incomes unsure if their water has been tested. Most rural Nebraskans do not treat their home tap water before drinking it. Persons living in or near the smallest communities (who were more likely to have private well water) are more likely than persons living in or near larger communities to not treat their home tap water. Rural Nebraskans have mixed opinions about various water problems. At least three in ten are concerned or very concerned about the following: contaminants in their water supply, water quality affecting their or their family’s health, water quality affecting wildlife or environment, water quality affecting the cost of water bills, and water will be too polluted. However, either the same or larger proportions indicate they are not concerned or not very concerned about these same items. Rural Nebraskans’ concerns about severe weather events have fluctuated over time. Concerns over extreme temperatures and more severe droughts declined between 2015 and 2020 but then increased again this year. The level of concern for these weather events this year is the highest over the three periods. Concerns about more severe droughts declined from 48 percent in 2015 to 21 percent in 2020 before increasing to 55 percent this year. However, when asked about more frequent extreme rains or floods, the level of concern was highest in 2020. Just under three in ten were concerned about extreme rains or floods in 2020, compared to just under one-quarter this year and 15 percent in 2015. In 2020, the flooding of 2019 was fresh in respondents’ minds. In 2015 parts of the state had been in drought the previous year and in 2022 most of the state is experiencing drought. These likely account for the differing levels of concerns between those years. This year, at least one-half of rural Nebraskans are concerned or very concerned about more severe droughts or dry periods (55%) and more extreme summer temperatures (50%). The Panhandle residents are more likely than residents of other regions to be concerned about more severe droughts or dry periods and more extreme summer temperatures. Rural Nebraskans are less likely to agree that we will learn to live with and adapt to climate change this year as they were in both 2013 and 2008. Just over six in ten agree with the statement this year, compared to just over seven in ten respondents in both 2013 and 2008. This year, most rural Nebraskans agree that we will learn to live with and adapt to climate change and that we have a responsibility to future generations to reduce the effects of climate change. A slight majority of rural Nebraskans agree that human activity is contributing to climate change. However, many rural Nebraskans agree that too much attention is paid to global climate change. This opinion was particularly apparent among persons with occupations in agriculture. Many rural Nebraskans favor proposals to reduce the effects of climate change that use tax credits or taxing corporations based on the carbon emissions they produce. Opinions are mixed on tougher carbon emission standards and tougher fuel-efficiency standards. Many rural Nebraskans oppose tax credits for electric vehicles

Disruption of Intraflagellar Transport in Adult Mice Leads to Obesity and Slow-Onset Cystic Kidney Disease

SummaryThe assembly of primary cilia is dependant on intraflagellar transport (IFT), which mediates the bidirectional movement of proteins between the base and tip of the cilium. In mice, congenic mutations disrupting genes required for IFT (e.g., Tg737 or the IFT kinesin Kif3a) are embryonic lethal, whereas kidney-specific disruption of IFT results in severe, rapidly progressing cystic pathology [1–3]. Although the function of primary cilia in most tissues is unknown, in the kidney they are mechanosenstive organelles that detect fluid flow through the tubule lumen [4]. The loss of this flow-induced signaling pathway is thought to be a major contributing factor to cyst formation [5–7]. Recent data also suggest that there is a connection between ciliary dysfunction and obesity as evidenced by the discovery that proteins associated with human obesity syndromes such as Alström and Bardet-Biedl localize to this organelle [8]. To more directly assess the importance of cilia in postnatal life, we utilized conditional alleles of two ciliogenic genes (Tg737 and Kif3a) to systemically induce cilia loss in adults. Surprisingly, the cystic kidney pathology in these mutants is dependent on the time at which cilia loss was induced, suggesting that cyst formation is not simply caused by impaired mechanosensation. In addition to the cystic pathology, the conditional cilia mutant mice become obese, are hyperphagic, and have elevated levels of serum insulin, glucose, and leptin. We further defined where in the body cilia are required for normal energy homeostasis by disrupting cilia on neurons throughout the central nervous system and on pro-opiomelanocortin-expressing cells in the hypothalamus, both of which resulted in obesity. These data establish that neuronal cilia function in a pathway regulating satiety responses

Resetting predator baselines in coral reef ecosystems

What did coral reef ecosystems look like before human impacts became pervasive? Early efforts to reconstruct baselines resulted in the controversial suggestion that pristine coral reefs have inverted trophic pyramids, with disproportionally large top predator biomass. The validity of the coral reef inverted trophic pyramid has been questioned, but until now, was not resolved empirically. We use data from an eight-year tag-recapture program with spatially explicit, capture-recapture models to re-examine the population size and density of a key top predator at Palmyra atoll, the same location that inspired the idea of inverted trophic biomass pyramids in coral reef ecosystems. Given that animal movement is suspected to have significantly biased early biomass estimates of highly mobile top predators, we focused our reassessment on the most mobile and most abundant predator at Palmyra, the grey reef shark (Carcharhinus amblyrhynchos). We estimated a density of 21.3 (95% CI 17.8, 24.7) grey reef sharks/km2, which is an order of magnitude lower than the estimates that suggested an inverted trophic pyramid. Our results indicate that the trophic structure of an unexploited reef fish community is not inverted, and that even healthy top predator populations may be considerably smaller, and more precarious, than previously thought

Robust relation between temporal discounting rates and body mass

When given the choice between $100 today and$110 in 1 week, certain people are more likely to choose the immediate, yet smaller reward. The present study examined the relations between temporal discounting rate and body mass while accounting for important demographic variables, depressive symptoms, and behavioral inhibition and approach. After having their heights and weights measured, 100 healthy adults completed the Monetary Choice Questionnaire, the Beck Depression Inventory-II, and the Behavioral Inhibition Scale/Behavioral Approach Scale. Overweight and obese participants exhibited higher temporal discounting rates than underweight and healthy weight participants. Temporal discounting rates decreased as the magnitude of the delayed reward increased, even when other variables known to impact temporal discounting rate (i.e., age, education level, and annual household income) were used as covariates. A higher body mass was strongly related to choosing a more immediate monetary reward. Additional research is needed to determine whether consideration-of-future-consequences interventions, or perhaps cognitive control interventions, could be effective in obesity intervention or prevention programs