Global, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties.

Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell. However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified. Here we present an integrated picture of the global ubiquitylation site occupancy and half-life. Ubiquitylation site occupancy spans over four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of phosphorylation. The occupancy, turnover rate, and regulation of sites by proteasome inhibitors are strongly interrelated, and these attributes distinguish sites involved in proteasomal degradation and cellular signaling. Sites in structured protein regions exhibit longer half-lives and stronger upregulation by proteasome inhibitors than sites in unstructured regions. Importantly, we discovered a surveillance mechanism that rapidly and site-indiscriminately deubiquitylates all ubiquitin-specific E1 and E2 enzymes, protecting them against accumulation of bystander ubiquitylation. The work provides a systems-scale, quantitative view of ubiquitylation properties and reveals general principles of ubiquitylation-dependent governance.

Heavy metal and trace element concentrations in the blood of scalloped hammerhead sharks (Sphyrna lewini) from La Paz Bay, México.

Sharks are particularly susceptible to bioaccumulation due to their life history characteristics and trophic position within marine ecosystems. Despite this, studies of bioaccumulation cover only a small proportion of extant species. In this study we report concentrations of trace elements and heavy metals in blood samples of Sphyrna lewini for the first time. We report high concentrations of several trace elements and heavy metals, with concentrations of some elements exceeding the limit determined safe for human consumption. High elemental concentrations may reflect biochemical differences between blood plasma and other tissues; however, they may also be symptomatic of high levels of exposure triggered by anthropogenic activities. We also provide evidence of elemental accumulation through ontogeny, the nature of which differs from that previously reported. Ultimately, this baseline study increases our understanding of interspecific and intraspecific variation in bioaccumulation and ecotoxicology in elasmobranchs which may prove important in ensuring adequate management.

Selection of climate variables in ant species distribution models: case study in South Korea.

The selection of explanatory variables is important in modeling prediction of changes in species distribution in response to climate change. In this study, we evaluated the importance of variable selection in species distribution models. We compared two different types of models for predicting the distribution of ant species: temperature-only and both temperature and precipitation. Ants were collected at 343 forest sites across South Korea from 2006 through 2009. We used a generalized additive model (GAM) to predict the future distribution of 16 species that showed significant responses to changes in climatic factors (temperature and/or precipitation). Four types of GAMs were constructed: temperature, temperature with interaction of precipitation, temperature and precipitation without interaction, and temperature and precipitation with interaction. Most species displayed similar results between the temperatureonly and the temperature and precipitation models. The results for predicted changes in species richness were different from the temperature-only model. This indicates higher uncertainty in the prediction of species richness, which is obtained by combining the prediction results of distribution change for each species, than in the prediction of distribution change. The turnover rate of the ant assemblages was predicted to increase with decreases in temperature and increases in elevation, which was consistent with other studies. Finally, our results showed that the prediction of the distribution or diversity of organisms responding to climate change is uncertain because of the high variability of the model outputs induced by the variables used in the models.

Multimodal assessment of brain fluid clearance is associated with amyloid-beta deposition in humans.

PURPOSE: The present study investigates a multimodal imaging assessment of glymphatic function and its association with brain amyloid-beta deposition. METHODS: Two brain CSF clearance measures (vCSF and DTI-ALPS) were derived from dynamic PET and MR diffusion tensor imaging (DTI) for 50 subjects, 24/50 were Aß positive (Aß+). T1W, T2W, DTI, T2FLAIR, and 11C-PiB and 18F-MK-6240 PET were acquired. Multivariate linear regression models were assessed with both vCSF and DTI-ALPS as independent variables and brain Aß as the dependent variable. Three types of models were evaluated, including the vCSF-only model, the ALPS-only model and the vCSF+ALPS combined model. Models were applied to the whole group, and Aß subgroups. All analyses were controlled for age, gender, and intracranial volume. RESULTS: Sample demographics (N=50) include 20 males and 30 females with a mean age of 69.30 (sd=8.55). Our results show that the combination of vCSF and ALPS associates with Aß deposition (p < 0.05, R2 = 0.575) better than either vCSF (p < 0.05, R2 = 0.431) or ALPS (p < 0.05, R2 = 0.372) alone in the Aß+ group. We observed similar results in whole-group analyses (combined model: p < 0.05, R2 = 0.287; vCSF model: p <0.05, R2 = 0.175; ALPS model: p < 0.05, R2 = 0.196) with less significance. Our data also showed that vCSF has higher correlation (r = -0.548) in subjects with mild Aß deposition and DTI-ALPS has higher correlation (r=-0.451) with severe Aß deposition subjects. CONCLUSION: The regression model with both vCSF and DTI-ALPS is better associated with brain Aß deposition. These two independent brain clearance measures may better explain the variation in Aß deposition than either term individually. Our results suggest that vCSF and DTI-ALPS reflect complementary aspects of brain clearance functions.

Determination of single-molecule transport activity of OATP2B1 by measuring the number of transporter molecules using electrophysiological approach.

Transporter-mediated clearance is determined by two factors, its single-molecule clearance, and expression level. However, no reliable method has been developed to evaluate them separately. This study aimed to develop a reliable method for evaluating the single-molecule activity of membrane transporters, such as organic anion transporting polypeptide (OATP) 2B1. HEK293 cells that co-expressed large conductance calcium-activated potassium (BK) channel and OATP2B1 were established and used for the following experiments. i) BK channel-mediated whole-cell conductance was measured using patch-clamp technique and divided by its unitary conductance to estimate the number of channels on plasma membrane (QI). ii) Using plasma membrane fraction, quantitative targeted absolute proteomics determined the stoichiometric ratio (ρ) of OATP2B1 to BK channel. iii) The uptake of estrone 3-sulfate was evaluated to calculate the Michaelis constant and uptake clearance (CL) per cell. Single-molecule clearance (CLint) was calculated by dividing CL by QI·ρ. QI and ρ values were estimated to be 916 and 2.16, respectively, yielding CLint of 5.23 fL/min/molecule. We successfully developed a novel method to reliably measure the single-molecule activity of a transporter, which could be used to evaluate the influences of factors such as genetic variations and post-translational modifications on the intrinsic activity of transporters.

Associations of vitamin B6 turnover rate with the risk of cardiovascular and all-cause mortality in hypertensive adults.

BACKGROUND AND AIM: This study was to assess the association between vitamin B6 turnover rate and mortality in hypertensive adults. METHODS AND RESULTS: Vitamin B6 status including serum pyridoxal-5'-phosphate (PLP) levels, serum 4-pyridoxal acid (4-PA) levels, and vitamin B6 turnover rate (4-PA/PLP) were obtained from the 2005-2010 National Health and Nutrition Examination Survey (NHANES) dataset of hypertensive adults with follow-up through December 30, 2019. Using Cox proportional risk regression models, Hazard ratios (HRs) and 95% confidence intervals (CIs) were analyzed for PLP, 4-PA and 4-PA/PLP quartiles in relation to cardiovascular and all-cause mortality. A total of 5434 participants were included in this study (mean age, 58.48 years; 50.4% men), and the median 4-PA/PLP was 0.75. The median follow-up time was 11.0 years, with 375 and 1387 cardiovascular and all-cause deaths, respectively. In multivariate COX regression models, PLP was negatively associated with cardiovascular mortality (HR [95% CI] quartile 4 vs. 1: 0.66 [0.47-0.94], Ptrend = 0.03) and 4-PA/PLP was positively associated with cardiovascular mortality (HR [95% CI] quartile 4 vs.1: 1.80 [1.21-2.67], Ptrend = 0.01). Similarly, the higher the quartile of PLP, the lower the risk of all-cause mortality (HR [95% CI] quartile 4 vs. 1: 0.67 [0.56-0.80], Ptrend < 0.01). The higher the quartile of 4-PA and 4-PA/PLP, the higher the risk of all-cause mortality (HR [95% CI] quartile 4 vs. 1: 1.22 [1.01-1.48], Ptrend < 0.01; and 2.09 [1.71-2.55], Ptrend < 0.01). CONCLUSION: The findings suggested that higher vitamin B6 turnover rate was associated with an increased risk of cardiovascular and all-cause mortality in hypertensive adults.

Modeling SILAC Data to Assess Protein Turnover in a Cellular Model of Diabetic Nephropathy.

Protein turnover rate is finely regulated through intracellular mechanisms and signals that are still incompletely understood but that are essential for the correct function of cellular processes. Indeed, a dysfunctional proteostasis often impacts the cell's ability to remove unfolded, misfolded, degraded, non-functional, or damaged proteins. Thus, altered cellular mechanisms controlling protein turnover impinge on the pathophysiology of many diseases, making the study of protein synthesis and degradation rates an important step for a more comprehensive understanding of these pathologies. In this manuscript, we describe the application of a dynamic-SILAC approach to study the turnover rate and the abundance of proteins in a cellular model of diabetic nephropathy. We estimated protein half-lives and relative abundance for thousands of proteins, several of which are characterized by either an altered turnover rate or altered abundance between diabetic nephropathic subjects and diabetic controls. Many of these proteins were previously shown to be related to diabetic complications and represent therefore, possible biomarkers or therapeutic targets. Beside the aspects strictly related to the pathological condition, our data also represent a consistent compendium of protein half-lives in human fibroblasts and a rich source of important information related to basic cell biology.

Cost-Effectiveness of Sugammadex Versus Neostigmine to Reverse Neuromuscular Blockade in a University Hospital in Taiwan: A Propensity Score-Matched Analysis.

Sugammadex has several pharmacological advantages over neostigmine, including faster reversal of neuromuscular blockade and fewer adverse effects. However, the economic impact of sugammadex remains controversial due to the considerable heterogeneity of study designs and clinical settings in previous studies. In a post-hoc analysis of a randomized controlled trial, we evaluated patients who underwent elective surgeries and general anesthesia with endotracheal intubation in a medical center in Taiwan between March 2020 and August 2020. Patients were divided into either the sugammadex or neostigmine group based on the neuromuscular blocking drug used. Propensity score matching was used to balance the baseline patient characteristics between the two groups. The patient's recovery from anesthesia and the putative cost-effectiveness of sugammadex versus neostigmine was assessed. Derived cost-effectiveness using personnel costs in the operating room and the post-anesthesia care unit was estimated using multiple linear regression models. A total of 2587 and 1784 patients were included before and after matching, respectively. Time to endotracheal extubation was significantly shorter in the sugammadex group (mean 6.0 ± standard deviation 5.3 min) compared with the neostigmine group (6.6 ± 6.3 min; p = 0.0032). In addition, the incidence of bradycardia was significantly lower in the sugammadex group (10.2%) compared with the neostigmine group (16.9%; p < 0.001). However, the total costs were significantly lower in the neostigmine group (50.6 ± 21.4 United States dollars) compared with the sugammadex group (212.0 ± 49.5 United States dollars). Despite improving postoperative recovery, the benefits of sugammadex did not outweigh its higher costs compared with neostigmine, possibly due to the low costs of labor in Taiwan's healthcare system.

Retention Time Alignment for Protein Turnover Studies Using Heavy Water Metabolic Labeling.

Retention time (RT) alignment has been important for robust protein identification and quantification in proteomics. In data-dependent acquisition mode, whereby the precursor ions are semistochastically chosen for fragmentation in MS/MS, the alignment is used in an approach termed matched between runs (MBR). MBR transfers peptides, which were fragmented and identified in one experiment, to a replicate experiment where they were not identified. Before the MBR transfer, the RTs of experiments are aligned to reduce the chance of erroneous transfers. Despite its widespread use in other areas of quantitative proteomics, RT alignment has not been applied in data analyses for protein turnover using an atom-based stable isotope-labeling agent such as metabolic labeling with deuterium oxide, D2O. Deuterium incorporation changes isotope profiles of intact peptides in full scans and their fragment ions in tandem mass spectra. It reduces the peptide identification rates in current database search engines. Therefore, the MBR becomes more important. Here, we report on an approach to incorporate RT alignment with peptide quantification in studies of proteome turnover using heavy water metabolic labeling and LC-MS. The RT alignment uses correlation-optimized time warping. The alignment, followed by the MBR, improves labeling time point coverage, especially for long labeling durations.

Metabolic deuterium oxide (D2O) labeling in quantitative omics studies: A tutorial review.

Mass spectrometry (MS) is an invaluable tool for sensitive detection and characterization of individual biomolecules in omics studies. MS combined with stable isotope labeling enables the accurate and precise determination of quantitative changes occurring in biological samples. Metabolic isotope labeling, wherein isotopes are introduced into biomolecules through biosynthetic metabolism, is one of the main labeling strategies. Among the precursors employed in metabolic isotope labeling, deuterium oxide (D2O) is cost-effective and easy to implement in any biological systems. This tutorial review aims to explain the basic principle of D2O labeling and its applications in omics research. D2O labeling incorporates D into stable C-H bonds in various biomolecules, including nucleotides, proteins, lipids, and carbohydrates. Typically, D2O labeling is performed at low enrichment of 1%-10% D2O, which causes subtle changes in the isotopic distribution of a biomolecule, instead of the complete separation between labeled and unlabeled samples in a mass spectrum. D2O labeling has been employed in various omics studies to determine the metabolic flux, turnover rate, and relative quantification. Moreover, the advantages and challenges of D2O labeling and its future prospects in quantitative omics are discussed. The economy, versatility, and convenience of D2O labeling will be beneficial for the long-term omics studies for higher organisms.

Perceived strategies for reducing staff-turnover and improving well-being and retention among professional caregivers in Alberta's continuing-care facilities: A qualitative study.

This qualitative study explored potential factors that lead to turnover and absenteeism and how to improve well-being and retention among professional older-adult-caregivers in Alberta's assisted living (AL) and long-term care (LTC) facilities. Four hundred and forty-seven participants aged 45-54 years were interviewed through a five-item, content-validated open-ended questionnaire. The questionnaire was self-administered in the English language and the soft copy of their responses was transferred into NVIVO version 12 software for coding. A thematic narrative analysis grounded in the "happy productive worker" theory was completed. The main themes were caregivers' perception of the factors affecting their well-being, absenteeism, and turnover, and caregivers' suggestions on ways to improve their well-being and retention. Participants reported that their professional well-being was suboptimal. They suggested that their employers should provide them with the needed social, psychological, and professional support, improve wages and hire more staff to ameliorate absenteeism and turnover rates.

Building a pharmacy technician structure for the future: A lesson from a multihospital academic health system.

PURPOSE: Over the past decade there has been increased attention on the need for highly skilled and trained pharmacy technicians; however, few best practices to assist health-system pharmacies in meeting technician workforce challenges have been identified. These challenges have been further revealed since 2019 through rising inflation, increased cost of living, and competing opportunities for skilled technical workers. This article describes an 18-hospital academic health system's experience implementing an innovative pharmacy technician career structure focused on increasing pharmacy technician engagement as well as improving recruitment and retention. METHODS: Prior to creating a new career structure, the department of pharmacy had one development track for pharmacy technicians, which included only 2 nonsupervisory job titles. Due to recruitment, retention, and employee engagement challenges, the department of pharmacy, in collaboration with the human resources department, developed a new pharmacy technician structure that included 3 pharmacy technician tracks and 4 nonsupervisory levels. Outcomes collected to determine the success of the program included pharmacy technician engagement survey scores, annual voluntary turnover rate, rolling 12-month voluntary turnover rate, monthly vacancy rate, and average years of service at termination. The monthly discharge prescription capture rate was also measured to support efforts to keep the cost of the new structure budget neutral. CONCLUSION: The change in career structure assisted in the improvement of each outcome identified. The close collaboration of the departments of pharmacy and human resources can lead to positive solutions of national problems and have a sustained impact on department operations.

DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates.

The enzyme turnover rate, ${k}_{cat}$, quantifies enzyme kinetics by indicating the maximum efficiency of enzyme catalysis. Despite its importance, ${k}_{cat}$ values remain scarce in databases for most organisms, primarily because of the cost of experimental measurements. To predict ${k}_{cat}$ and account for its strong temperature dependence, DLTKcat was developed in this study and demonstrated superior performance (log10-scale root mean squared error = 0.88, R-squared = 0.66) than previously published models. Through two case studies, DLTKcat showed its ability to predict the effects of protein sequence mutations and temperature changes on ${k}_{cat}$ values. Although its quantitative accuracy is not high enough yet to model the responses of cellular metabolism to temperature changes, DLTKcat has the potential to eventually become a computational tool to describe the temperature dependence of biological systems.

Air pollution, investor sentiment and stock liquidity.

With the aggravation of air pollution, the impact of air pollution on the stock market, especially from the perspective of investor sentiment, has been of great concern and widely discussed. Based on data from China's A-share listed firms from January 1, 2016, to December 31, 2020, the relationship between urban air pollution and stock liquidity of listed firms and the internal mechanism is examined. Firstly, based on local preference theory, we start by predicting the impact of air pollution on stock liquidity. We, then, build a regression model for air pollution and stock liquidity, introducing the intermediary effect model to detect the relationship between the two and its mechanism. Finally, by subdividing the samples, we discuss the differential impact of air pollution on stock liquidity under different circumstances. We found that when air pollution worsens it reduces stock liquidity. The results of the mechanism analysis show that investor sentiment plays an intermediary role in the process of air pollution affecting stock liquidity, and pessimism induced by air pollution can reduce stock liquidity. Heterogeneity test results show that there are differences in the impact of air pollution on stock liquidity between heavily polluting firms and non-heavily polluting firms, different industries, different city sizes, and different levels of air pollution, has a greater effect in non-heavily polluting enterprises, manufacturing and other industries, medium sized cities and light pollution. The results of this research have important reference value for environmental protection departments to establish and improve air pollution monitoring systems and for listed firms to improve stock liquidity and deal with the environmental financial risks appropriately.

Demography: Fast and Slow.

Scientific ideas on the human population tend to be rooted in a "slow demography" paradigm, which emphasizes an inertial, predictable, self-contained view of population dynamics, mostly dependent on fertility and mortality. Yet, demography can also move fast. At the country level, it is crucial to empirically assess how fast demography moves by taking migratory movements into account, in addition to fertility and mortality. We discuss these ideas and present new estimates of the speed of population change, that is, country-level population turnover rates, as well as the share of turnover due to migration, for all countries in the world with available data between 1990 and 2020. Population turnover is inversely related to population size and development, and migratory movements tend to become important factors in shaping demography for both small and highly developed countries. Longitudinally, we analyze annual turnover data for Italy and Germany, documenting the changing speed of population change over time and its determinants. Accepting the "fast and slow" demography perspective has several implications for science and policy, which we discuss.

Experimentally derived biochemical modelling parameters to improve understanding of aquaculture's effect on marine food webs.

To construct robust biogeochemical models for application to marine-based aquaculture settings, careful selection of appropriate model parameters is necessary. This study used an experimental approach to establish biomarkers of farm and marine-derived organic matter, and to derive isotopic turnover rates, and trophic discrimination factors specific to aquaculture associated food webs. A shift towards a farm-derived resource base resulted in consumer tissues more depleted in the carbon-13 isotope (indicated by more negative δ13C values) and a higher proportion of oleic acid, linoleic acid, and alpha-linoleic acid in the fatty acid profile of consumers over time. Measured trophic discrimination factors between dietary sources and consumer tissues demonstrated high variability among species and tissue types, ranging from -0.25‰ to 0.82‰ for Δ13C and from -0.77‰ to 6.8‰ for Δ15N. Stable isotope half-lives were also diverse among species and tissue types, ranging from <7 days to 462 days. Results demonstrated that construction of robust models for tracing assimilation of farm-derived organic matter through marine food webs requires the use of taxa and tissue specific parameters. Turnover rates have applications for understanding assimilative capacity of communities and for managing populations within the ecological footprint of farms.

Transport Turnover Rates for Human OCT2 and MATE1 Expressed in Chinese Hamster Ovary Cells.

MATE1 (multidrug and toxin extruder 1) and OCT2 (organic cation transporter 2) play critical roles in organic cation excretion by the human kidney. The transporter turnover rate (TOR) is relevant to understanding both their transport mechanisms and interpreting the in vitro-in vivo extrapolation (IVIVE) required for physiologically-based pharmacokinetic (PBPK) modeling. Here, we use a quantitative western blot method to determine TORs for MATE1 and OCT2 proteins expressed in CHO cells. MATE1 and OCT2, each with a C-terminal V-5 epitope tag, were cell surface biotinylated and the amount of cell surface MATE1 and OCT2 protein was quantified by western analysis, using standard curves for the V5 epitope. Cell surface MATE1 and OCT2 protein represented 25% and 24%, respectively, of the total expression of these proteins in CHO cells. The number of cell surface transporters was ~55 fmol cm-2 for MATE1 and ~510 fmol cm-2 for OCT2. Dividing these values into the different Jmax values for transport of MPP, metformin, and atenolol mediated by MATE1 and OCT2 resulted in calculated TOR values (±SE, n = 4) of 84.0 ± 22.0 s-1 and 2.9 ± 0.6 s-1; metformin, 461.0 ± 121.0 s-1 and 12.6 ± 2.4 s-1; atenolol, 118.0 ± 31.0 s-1, respectively. These values are consistent with the TOR values determined for a variety of exchangers (NHEs), cotransporters (SGLTs, Lac permease), and uniporters (GLUTs, ENTs).

Effects of Physical Properties and Processing Methods on Astragaloside IV and Flavonoids Content in Astragali radix.

The aim of this study was to investigate the effects of the physical properties (diameter size, powder particle size, composition of bark- and wood-tissue, and turnover rate) and processing methods on the content of active ingredients in Astragali radix (AR), a popular Chinese herbal medicine. The astragaloside IV and flavonoid contents increased with decreasing diameter size. Bark-tissue had significantly higher astragaloside IV and formononetin content than that in the wood-tissue. As a higher proportion of bark-tissue is associated with decreasing diameter, a strong correlation was also shown between bark- to wood-tissue ratio and active ingredients' content. Furthermore, an increase in astragaloside IV content was observed in thin powder as compared to coarse powder ground from the whole root. However, this association between active ingredients' content and powder particle size was abolished when isolating bark- and wood-tissue individually. Moreover, AR stir-frying with refined honey, a typical processing method of AR, increased formononetin content. The turnover rate of active constituents upon decoction ranged from 61.9-81.4%. Assessing the active constituent contents using its physical properties and processing methods allows for a more comprehensive understanding of optimizing and strengthening the therapeutic potentials of AR used in food and herbal supplements.

Why Do They Leave? The Counterplans to Continue Working among Preschool Workers in Japan: A Cross-Sectional Survey.

Three institutions predominantly care for preschool children in Japan: kindergartens, authorized childcare institutions, and nursery centers. Recently, the turnover rates of preschool workers in these institutions have been high, and Japan has been facing a shortage of kindergarten teachers. The study aimed to provide concrete counterplans to reduce preschool workers' turnover rate. To determine the causes of turnover, we conducted a cross-sectional survey. We recruited preschool workers from several kindergartens, authorized childcare institutions, and nursery centers in Japan to fill out a survey regarding counterplans for employment. Of the 1002 surveys, 551 (541 women; 10 men) complete surveys were received (response rate: 55%). A total of 295 participants answered that they were unwilling to continue working for longer than five years and completed the questionnaires. The Jiro Kawakita method was used to categorize and analyze the four sections of the counterplan questionnaires. The results showed that the main reasons for high turnover were overtime work, low salary, and difficult human relations. To solve these issues, the counterplan ideas such as workshop ideas and conditions conducive to continuing working longer were related to human relations, work conditions, and mental health.

Low Efficiency in a Five-Year Hospital Performance Assessment According to Pabon Lasso Model: State-Affiliated Hospitals of Abadan.

BACKGROUND: A hospital consumes a large amount of health resources, and investigating hospital performance can increase hospital efficiency. METHOD: This retrospective descriptive research analyzed data on performance of 6 hospitals in Abadan, Iran, during a five-year period (2015-2019), based on Graphical Model of Pabon Lasso. RESULTS: Findings suggested 16% of studied hospitals were in Zone 1, 50% were in Zone 3, and 33% were in Zone 4 of the Model. None of the hospitals were in Zone 2. CONCLUSION: As the hospitals in this study did not perform efficiently, concerns related to more efficiently use of available resources are crucial.