The expected changes with different periods of home-based resistance exercise in patients with chronic kidney disease.

BACKGROUND: The comprehensive impact of prolonged home-based resistance training on individuals grappling with chronic kidney disease (CKD) have yet to be fully elucidated. This study aimed to explore the outcomes of varying exercise durations on physical performance, nutritional status, and kidney function within this specific population, encompassing patients undergoing dialysis and those affected by severe sarcopenia. METHODS: This was a 1-year observational double cohort study following a 52-week longitudinal design, we enrolled 101 adult CKD outpatients. These participants were divided into two groups: the continuous group, comprising individuals who consistently exercised for over 6 months, and the interrupted group, which included those who did not sustain regular exercise for the same duration. The exercise regimen involved resistance exercises conducted at least 3 to 5 days per week, involving activities like lifting dumbbells and executing weighted wall squats. Physical activity assessments and biochemical blood tests were conducted at weeks 0, 4, 16, 28, 40, and 52 for all participants. RESULTS: The continuous exercise group exhibited better handgrip strength and sit-to-stand movement compared to the interrupted group. Their estimated glomerular filtration rate stayed steady while the interrupted group was declined. Additionally, those who exercised consistently had better metabolism: higher carbon dioxide levels, increased albumin, better nutritional scores, and lower levels of blood urea nitrogen, creatinine, fasting blood glucose, and body weight. Subsequent adjustments for potential confounding factors continued to show improved physical performance and kidney function over time. CONCLUSION: Our findings indicate the advantageous impact of extended resistance exercise training on overall health of CKD patients, even those on dialysis or with severe sarcopenia. Dedication to this exercise routine could improve kidney function, metabolism, and physical abilities in these patients.

Clinical analysis of PAFAH1B1 gene variants in pediatric patients with epilepsy.

PURPOSE: PAFAH1B1, also known as LIS1, is associated with type I lissencephaly in humans, which is a severe developmental brain disorder believed to result from abnormal neuronal migration. Our objective was to characterize the genotypes and phenotypes of PAFAH1B1-related epilepsy. METHODS: We conducted a comprehensive analysis of the medical histories, magnetic resonance imaging findings, and video-electroencephalogram recordings of 11 patients with PAFAH1B1 variants at the Neurology Department of Beijing Children's Hospital from June 2017 to November 2022. RESULTS: The age of onset of epilepsy ranged from 2 months to 4 years, with a median onset age of 5 months. Among these 11 patients (comprising 6 boys and 5 girls), all were diagnosed with lissencephaly type 1. Predominantly, generalized tonic-clonic and spasm seizures characterized PAFAH1B1-related epilepsy. Additionally, 10 out of the 11 patients exhibited severe developmental disorders. All patients exhibited de novo variants, with three individuals displaying 17p13.3 deletions linked to haploinsufficiency of PAFAH1B1. Four variants were previously unreported. Notably, three patients with 17p13.3 deletions displayed developmental delay and drug resistant epilepsy, whereas the single patient with mild developmental delay, Intelligence Quotient (IQ) 57 and well-controlled seizures had a splicing-site variant. CONCLUSION: The severity of the phenotype in patients with PAFAH1B1 variants ranged from drug-responsive seizures to severe epileptic encephalopathy. These observations underscore the clinical heterogeneity of PAFAH1B1-related disorders, with most patients exhibiting developmental disorders. Moreover, the severity of epilepsy appears to be linked to genetic variations.

The Role of Lifestyle Intervention, in Addition to Drugs, for Diabetic Kidney Disease with Sarcopenic Obesity.

Diabetic kidney disease is the leading cause of end-stage renal disease in developing and developed countries. The growing prevalence and clinical challenges of sarcopenic obesity have been associated with the frailty and disability of diabetic kidney disease. It has been reported that insulin resistance, chronic inflammation, enhanced oxidative stress and lipotoxicity contribute to the pathophysiology of muscle loss and visceral fat accumulation. Sarcopenic obesity, which is diagnosed with dual-energy X-ray absorptiometry, is associated with worse outcomes in kidney disease. Growing evidence indicates that adherence to healthy lifestyles, including low protein diet, proper carbohydrate control, vitamin D supplement, and regular physical training, has been shown to improve clinical prognosis. Based on the higher risk of sarcopenic-obesity-related renal function decline, it has led to the exploration and investigation of the pathophysiology, clinical aspects, and novel approach of these controversial issues in daily practice.

Impacts of model resolution and ocean coupling on mean and eddy momentum transfer during the rapid intensification of super-typhoon Muifa (2011).

This study uses a coupled atmosphere-ocean model with different numerical settings to investigate the mean and eddy momentum transfer processes responsible for Typhoon Muifa's (2011) early rapid intensification (RI). Three experiments are conducted. Two use the coupled model with a horizontal resolution of either 1 km (HRL) or 3 km (LRL). The third (NoTCFB) is the same as LRL but excludes tropical cyclone (TC)-induced sea-surface temperature (SST) cooling. HRL reasonably reproduces Muifa's intensity during its rapid intensification and weakening periods. The azimuthal mean tangential and radial momentum budgets are analysed before the RI rates diverge between HRL and LRL. Results show that the dominant processes responsible for Muifa's intensification are different in HRL and LRL. For HRL, the net eddy effect intensifies the storm's circulation and contracts the eyewall during early RI, and it dominates the net mean-flow effect inside the radius of maximum wind (RMW), except near the surface and between 2 and 5 km close to the RMW. In contrast, the mean and eddy effects in LRL almost cancel inside the RMW, while the mean-flow effects dominate and intensify tangential winds outside. Without TC-induced SST cooling, Muifa in NoTCFB reaches a similar storm intensity as in HRL but its rapid weakening rate is substantially underestimated. The dominant mechanisms for tangential wind intensification in NoTCFB are similar to those in LRL, but their magnitudes are larger, implying a misrepresentation of the dominant momentum transfer processes in NoTCFB during RI. For the radial momentum budget analysis, the dominant processes are similar among the three experiments except for some differences in their locations and strengths.

Impacts of Saharan Mineral Dust on Air-Sea Interaction over North Atlantic Ocean Using a Fully Coupled Regional Model.

This study examines the modifications of air-sea coupling processes by dust-radiation-cloud interactions over the North Atlantic Ocean using a high-resolution coupled atmosphere-wave-ocean-dust (AWOD) regional model. The dust-induced mechanisms that are responsible for changes of sea surface temperature (SST) and latent and sensible heat fluxes (LHF/SHF) are also examined. Two 3-month numerical experiments are conducted, and they differ only in the activation and deactivation of dust-radiation-cloud interactions. Model results show that the dust significantly reduces surface downward radiation fluxes (SDRF) over the ocean with the maximum change of 20-30 W m-2. Over the dust plume region, the dust effect creates a low-pressure anomaly and a cyclonic circulation anomaly, which drives a positive wind stress curl anomaly, thereby reducing sea surface height and mixed layer depth. However, the SST change by dust, ranging from -0.5 to 0.5 K, has a great spatial variation which differs from the dust plume shape. Dust cools SST around the West African coast, except under the maximum dust plume ridge, and extends westward asymmetrically along the northern and southern edges of the dust plume. Dust unexpectedly warms SST over a large area of the western tropical North Atlantic and north of the dust plume. These SST changes are controlled by different mechanisms. Unlike the SST change pattern, the LHF and SHF changes are mostly reduced underneath the dust plume region, though they are different in detail due to different dominant factors, and increased south of the dust plume over the tropic.

Evaluating the Impact of Assimilating Aerosol Optical Depth Observations on Dust Forecasts Over North Africa and the East Atlantic Using Different Data Assimilation Methods.

This study evaluates the impact of assimilating moderate resolution imaging spectroradiometer (MODIS) aerosol optical depth (AOD) data using different data assimilation (DA) methods on dust analyses and forecasts over North Africa and tropical North Atlantic. To do so, seven experiments are conducted using the Weather Research and Forecasting dust model and the Gridpoint Statistical Interpolation analysis system. Six of these experiments differ in whether or not AOD observations are assimilated and the DA method used, the latter of which includes the three-dimensional variational (3D-Var), ensemble square root filter (EnSRF), and hybrid methods. The seventh experiment, which allows us to assess the impact of assimilating deep blue AOD data, assimilates only dark target AOD data using the hybrid method. The assimilation of MODIS AOD data clearly improves AOD analyses and forecasts up to 48 hr in length. Results also show that assimilating deep blue data has a primarily positive effect on AOD analyses and forecasts over and downstream of the major North African source regions. Without assimilating deep blue data (assimilating dark target only), AOD assimilation only improves AOD forecasts for up to 30 hr. Of the three DA methods examined, the hybrid and EnSRF methods produce better AOD analyses and forecasts than the 3D-Var method does. Despite the clear benefit of AOD assimilation for AOD analyses and forecasts, the lack of information regarding the vertical distribution of aerosols in AOD data means that AOD assimilation has very little positive effect on analyzed or forecasted vertical profiles of backscatter.

Identification of Salmonella Taxon-Specific Peptide Markers to the Serovar Level by Mass Spectrometry.

We present an LC-MS/MS pipeline to identify taxon-specific tryptic peptide markers for the identification of Salmonella at the genus, species, subspecies, and serovar levels of specificity. Salmonella enterica subsp. enterica serovars Typhimurium and its four closest relatives, Saintpaul, Heidelberg, Paratyphi B, and Muenchen, were evaluated. A decision-tree approach was used to identify peptides common to the five Salmonella proteomes for evaluation as genus-, species-, and subspecies-specific markers. Peptides identified for two or fewer Salmonella strains were evaluated as potential serovar markers. Currently, there are approximately 140 000 assembled bacterial genomes publicly available, more than 8500 of which are for Salmonella. Consequently, the specificity of each candidate peptide marker was confirmed across all publicly available protein sequences in the NCBI nonredundant (nr) database. The performance of a subset of candidate taxon-specific peptide markers was evaluated in a targeted mass-spectrometry method. The presented workflow offers a marked improvement in specificity over existing MALDI-TOF-based bacterial identification platforms for the identification of closely related Salmonella serovars.

Association between trace element concentrations and anemia in patients with chronic kidney disease: a cross-sectional population-based study.

Anemia is common in chronic kidney disease (CKD) and may be affected by trace element concentrations. While the concentrations of trace elements are known to be altered in CKD, the relationship between trace element and hemoglobin concentrations has not been systematically investigated in a large cohort. This study aims to examine associations between trace element concentrations and anemia in patients with CKD. Data from the National Health and Nutrition Examination Survey collected from 2011 to 2014 were used for this analysis. The participants who were more than 20 years old were included. A total of 3057 participants were included; the final cohort was divided into two groups based on CKD status. The concentrations of hemoglobin, iron, zinc, and manganese were significantly lower in participants with than without CKD (all p<0.05). Multivariate analyses showed that in patients without CKD, hemoglobin concentrations correlated positively with iron, zinc, and cadmium (ß=0.005, 0.009, and 0.33, respectively), but correlated negatively with copper levels (ß=-0.002). In patients with CKD, hemoglobin concentrations correlated positively with cadmium and selenium, but negatively with copper levels (ß=0.57, 0.007, and -0.008, respectively). The serum iron concentration was found to correlate positively with zinc, cadmium, and selenium, but negatively with copper and manganese concentrations in the total study population (all p<0.05). The associations between serum concentrations of trace elements and hemoglobin differ between patients with and without CKD. Further investigations are warranted to determine whether patients with CKD have distinct trace element requirements.

Relationship between the social support and self-efficacy for function ability in patients undergoing primary hip replacement.

BACKGROUND: The World Health Organization (WHO) reported that nearly 25% of people will suffer from physical disability owing to the bone and joint problems until 2050. The condition of patients with this type of difficulty could be improved by increasing positive self-efficacy and instigating suitable medical treatment to implement self-efficacy for functional ability (SEFA) and physical functional ability self-care. In this study, we aim to evaluate the influence of social support on SEFA in patients after total hip arthroplasty. METHODS: This cross-sectional study used structural questionnaires, telephone appointments, and data collection to obtain patient characteristics, such as gender, age, educational level, and marital status. Questionnaires about social support and self-efficacy for functional ability (SEFA) were sent to 200 patients at 3 months following a primary total hip replacement from September 2011 to December 2014. Factor analysis was used to categorize the dimensions of social support; the t test, analysis of variance (ANOVA), and correlation analysis were applied to screen factors influencing SEFA. Multiple regression analysis was employed to ascertain the relationships between patient characteristics, social support, and SEFA. RESULTS: In total, 134 patients responded to the questionnaires. Lower SEFA scores were observed in patients of an older age, unmarried patients, and those with a low level of education. Correlation analysis showed that emotional information and appraisal support, instrumental support, and SEFA were positively correlated. Multiple regression analysis was applied to ascertain the relationships between patient characteristics, social support, and SEFA. We identified significant coefficient values of - 0.187 for age, 5.344 for emotional information and appraisal support, and 1.653 for instrumental support. CONCLUSION: The results of this study demonstrated that in patients undergoing primary hip replacement, positive impacts on SEFA were observed in relation to emotional information, appraisal support and instrumental support. The results indicated that enhancing emotional information and appraisal support could improve a patient's self-efficacy for functional ability.

[Glucose transporter 1 deficiency syndrome: features of movement disorders, diagnosis and treatment].

OBJECTIVE: To investigate the clinical features, diagnosis and treatment of glucose transporter 1 deficiency syndrome (GLUT1-DS), as well as the diagnostic value of movement disorders. METHODS: The clinical data of four children with GLUT1-DS were collected, and their clinical features, treatment, and follow-up results were analyzed. RESULTS: There were two boys and two girls, with an age of onset of 2-15 months. Clinical manifestations included movement disorders, seizures, and developmental retardation. Seizures were the cause of the first consultation in all cases. The four children all had persistent ataxia, dystonia, and dysarthria; two had persistent tremor, two had paroxysmal limb paralysis, and two had eye movement disorders. Paroxysmal symptoms tended to occur in fatigue state. All four children had reductions in the level of cerebrospinal fluid glucose and its ratio to blood glucose, as well as SLC2A1 gene mutations. The four children were given a ketogenic diet, at a ketogenic ratio of 2:1 to 3:1, and achieved complete remission of paroxysmal symptoms within 5 weeks. CONCLUSIONS: GLUT1-DS should be considered for epileptic children with mental retardation and motor developmental delay complicated by various types of movement disorders. The ketogenic diet is effective at a ketogenic ratio of 2:1 to 3:1 for the treatment of GLUT1-DS.

Exploring the expression bar code of SAA variants for gastric cancer detection.

We reported an integrated platform to explore serum protein variant pattern in cancer and its utility as a new class of biomarker panel for diagnosis. On the model study of serum amyloid A (SAA), we employed nanoprobe-based affinity mass spectrometry for enrichment, identification and quantitation of SAA variants from serum of 105 gastric cancer patients in comparison with 54 gastritis patients, 54 controls, and 120 patients from other cancer. The result revealed surprisingly heterogeneous and most comprehensive SAA bar code to date, which comprises 24 SAA variants including SAA1- and SAA2-encoded products, polymorphic isoforms, N-terminal-truncated forms, and three novel SAA oxidized isotypes, in which the variant-specific peptide sequence were also confirmed by LC-MS/MS. A diagnostic model was developed for dimension reduction and computational classification of the 24 SAA-variant bar code, providing good discrimination (AUC = 0.85 ± 3.2E-3) for differentiating gastric cancer group from gastritis and normal groups (sensitivity, 0.76; specificity, 0.81) and was validated with external validation cohort (sensitivity, 0.71; specificity, 0.74). Our platform not only shed light on the occurrence and modification extent of under-represented serum protein variants in cancer, but also suggested a new concept of diagnostic platform by serum protein variant profile.

Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein.

Hepatitis C virus (HCV) encodes mechanisms to evade the multilayered antiviral actions of the host immune system. Great progress has been made in elucidating the strategies HCV employs to down-regulate interferon (IFN) production, impede IFN signaling transduction, and impair IFN-stimulated gene (ISG) expression. However, there is a limited understanding of the mechanisms governing how viral proteins counteract the antiviral functions of downstream IFN effectors due to the lack of an efficient approach to identify such interactions systematically. To study the mechanisms by which HCV antagonizes the IFN responses, we have developed a high-throughput profiling platform that enables mapping of HCV sequences critical for anti-IFN function at high resolution. Genome-wide profiling performed with a 15-nt insertion mutant library of HCV showed that mutations in the p7 region conferred high levels of IFN sensitivity, which could be alleviated by the expression of WT p7 protein. This finding suggests that p7 protein of HCV has an immune evasion function. By screening a liver-specific ISG library, we identified that IFI6-16 significantly inhibits the replication of p7 mutant viruses without affecting WT virus replication. In contrast, knockout of IFI6-16 reversed the IFN hypersensitivity of p7 mutant virus. In addition, p7 was found to be coimmunoprecipitated with IFI6-16 and to counteract the function of IFI6-16 by depolarizing the mitochondria potential. Our data suggest that p7 is a critical immune evasion protein that suppresses the antiviral IFN function by counteracting the function of IFI6-16.

Modifier-assisted differential mobility-tandem mass spectrometry method for detection and quantification of amphetamine-type stimulants in urine.

An advantage of differential mobility spectrometry (DMS) is it provides an orthogonal mechanism to mass spectrometry (MS). The DMS-MS/MS detects analytes in the gas phase on the basis of differences in ion mobility in low and high electric fields, which makes DMS-MS/MS an alternative to chromatographic separation-MS. One drawback of DMS is its limited resolution and sensitivity, especially for detecting small molecules when using a nonpolar inert gas as the carrier gas. The present work has evaluated the effects on peak capacity of adding chemical modifiers to inert carrier gases (nitrogen, helium, argon and carbon dioxide). Use of a methanol-helium mixture gave improvements in both separation and sensitivity. Nine structurally similar amphetamine-type stimulants were determined in urine without pretreatment of the samples before analysis. After optimization of carrier gas, nature and concentration of chemical modifier, and DMS temperature, limits of detection ranging from 1.1 to 2.7 ng mL-1, with a linear range of three orders of magnitude (5-5000 ng mL-1) were achieved. Precision was <15% and the accuracy of the quality control samples was 87.6-113.7%. For the quantitation of urine samples from drug abusers, data obtained using DMS-MS/MS showed reasonable agreement (within ±19.5%) with that obtained using LC-MS/MS. The analysis time for DMS-MS/MS was only 1.1 min and a paired sample t-test between the two methods gave a p-value of 0.0894, which indicates that DMS-MS/MS is a reliable method, with comparable precision and sensitivity to LC-MS/MS.

Reaction of Human Cd7metallothionein and N-Ethylmaleimide: Kinetic and Structural Insights from Electrospray Ionization Mass Spectrometry.

The reaction of cadmium-binding human metallothionein-2A (Cd7MT) and N-ethylmaleimide (NEM) is investigated by electrospray ionization-ion mobility-mass spectrometry (ESI IM-MS). MS provides a direct measure of the distribution of the kinetic intermediates as the reaction proceeds and provides new insights into the relative kinetic stability of the individual metal-thiolate bonds in Cd7MT. The rate constants for the various metal-retaining intermediates (Cd(i), intermediate with i Cd²âº ions attached) differ by >3 orders of magnitude: Cd4< Cd3< Cd2< Cd1∼ Cd6 < Cd7 < Cd5. The reaction is viewed as a two-component cooperative process, rapid loss of three Cd²âº ions followed by slow loss of the remaining four Cd²âº ions, and Cd4NEM10MT was observed as the least reactive intermediate during the entire displacement process. "MS-CID-IM-MS", a top-down approach that provides two-dimensional dispersion (size to charge by IM; mass to charge by MS) of the CID fragment ions, was used for direct analysis of the kinetic intermediate [Cd4NEM10MT]5⁺ ion. The results provide direct evidence that the four Cd²âº ions located in the α-domain are retained, indicative of the greater kinetic stability for the α-domain. Further, the mapping of the alkylation sites in the [Cd4NEM10MT]5⁺ ion reveals that not only the nine cysteines in the ß-domain but Cys33 in the α-domain is selectively labeled. The kinetic lability of the Cd-Cys33 bond is unexpected. The structural and functional implications of these findings are discussed.

How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures?

Here, we critically evaluate the effects of changes in the ion internal energy (E(int)) on ion-neutral collision cross sections (CCS) of ions of two structurally diverse proteins, specifically the [M + 6H](6+) ion of ubiquitin (ubq(6+)), the [M + 5H](5+) ion of the intrinsically disordered protein (IDP) apo-metallothionein-2A (MT), and its partially- and fully-metalated isoform, the [CdiMT](5+) ion. The ion-neutral CCS for ions formed by "native-state" ESI show a strong dependence on E(int). Collisional activation is used to increase E(int) prior to the ions entering and within the traveling wave (TW) ion mobility analyzer. Comparisons of experimental CCSs with those generated by molecular dynamics (MD) simulation for solution-phase ions and solvent-free ions as a function of temperature provide new insights about conformational preferences and retention of solution conformations. The E(int)-dependent CCSs, which reveal increased conformational diversity of the ion population, are discussed in terms of folding/unfolding of solvent-free ions. For example, ubiquitin ions that have low internal energies retain native-like conformations, whereas ions that are heated by collisional activation possess higher internal energies and yield a broader range of CCS owing to increased conformational diversity due to losses of secondary and tertiary structures. In contrast, the CCS profile for the IDP apoMT is consistent with kinetic trapping of an ion population composed of a wide range of conformers, and as the E(int) is increased, these structurally labile conformers unfold to an elongated conformation.

Low-density lipoprotein electronegativity is a novel cardiometabolic risk factor.

BACKGROUND: Low-density lipoprotein (LDL) plays a central role in cardiovascular disease (CVD) development. In LDL chromatographically resolved according to charge, the most electronegative subfraction-L5-is the only subfraction that induces atherogenic responses in cultured vascular cells. Furthermore, increasing evidence has shown that plasma L5 levels are elevated in individuals with high cardiovascular risk. We hypothesized that LDL electronegativity is a novel index for predicting CVD. METHODS: In 30 asymptomatic individuals with metabolic syndrome (MetS) and 27 healthy control subjects, we examined correlations between plasma L5 levels and the number of MetS criteria fulfilled, CVD risk factors, and CVD risk according to the Framingham risk score. RESULTS: L5 levels were significantly higher in MetS subjects than in control subjects (21.9±18.7 mg/dL vs. 11.2±10.7 mg/dL, P:0.01). The Jonckheere trend test revealed that the percent L5 of total LDL (L5%) and L5 concentration increased with the number of MetS criteria (P<0.001). L5% correlated with classic CVD risk factors, including waist circumference, body mass index, waist-to-height ratio, smoking status, blood pressure, and levels of fasting plasma glucose, triglyceride, and high-density lipoprotein. Stepwise regression analysis revealed that fasting plasma glucose level and body mass index contributed to 28% of L5% variance. The L5 concentration was associated with CVD risk and contributed to 11% of 30-year general CVD risk variance when controlling the variance of waist circumference. CONCLUSION: Our findings show that LDL electronegativity was associated with multiple CVD risk factors and CVD risk, suggesting that the LDL electronegativity index may have the potential to be a novel index for predicting CVD. Large-scale clinical trials are warranted to test the reliability of this hypothesis and the clinical importance of the LDL electronegativity index.

Metal-induced conformational changes of human metallothionein-2A: a combined theoretical and experimental study of metal-free and partially metalated intermediates.

Electrospray ionization ion mobility mass spectrometry (ESI IM-MS) and molecular dynamics (MD) simulations reveal new insights into metal-induced conformational changes and the mechanism for metalation of human metallothionein-2A (MT), an intrinsically disordered protein. ESI of solutions containing apoMT yields multiple charge states of apoMT; following addition of Cd(2+) to the solution, ESI yields a range of CdiMT (i = 1-7) product ions (see Chen et al. Anal. Chem. 2013, 85, 7826-33). Ion mobility arrival-time distributions (ATDs) for the CdiMT (i = 0-7) ions reveal a diverse population of ion conformations. The ion mobility data clearly show that the conformational diversity for apoMT and partially metalated ions converges toward ordered, compact conformations as the number of bound Cd(2+) ions increase. MD simulations provide additional information on conformation candidates of CdiMT (i = 0-7) that supports the convergence of distinct conformational populations upon metal binding. Integrating the IM-MS and MD data provides a global view that shows stepwise conformational transition of an ensemble as a function of metal ion bound. ApoMT is comprised of a wide range of conformational states that populate between globular-like compact and coil-rich extended conformations. During the initial stepwise metal addition (number of metal ions bound i = 1-3), the metal ions bind to different sites to yield distinct conformations, whereas for i > 4, the conformational changes appear to be domain-specific, attributed to different degrees of disorder of the ß domain; the ß domain becomes more ordered as additional metal ions are added, promoting convergences to the dumbbell-shaped conformation.

A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity.

Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG) approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A) on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients.