De novo design of high-affinity binders of bioactive helical peptides.

Many peptide hormones form an α-helix on binding their receptors1-4, and sensitive methods for their detection could contribute to better clinical management of disease5. De novo protein design can now generate binders with high affinity and specificity to structured proteins6,7. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion8 to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.

Investigation of The Alleviating Effect of Liquid Seaweed Fertilizer on Lavandula officinalis under Salt Stress.

Sustainable practices in plant production involve various environmental methods that improve the urban ecosystem by preserving both natural resources and biological diversity. Organic material application against salt stress is one of the most important sustainable practices. The purpose of this study was to explore how various traits of Lavandula officinalis under salt stress were affected by seaweed liquid. To this end, the experiment was performed as a completely randomized experimental design with two factors including four replications under greenhouse conditions. In the experiments, salt concentrations were prepared as control (distilled water), 40 mM and 80 mM NaCl, and seaweed liquid levels were applied as control (0%) - 0.5%-1%-2% and 4%. L. officinalis was considerably negatively affected by salt stress in terms of its quality, growth, photosynthetic and biochemical traits. According to the results of this empirical research, seaweed liquid application was the alleviating factor in negative effects in all traits resulting from the increase in NaCl concentrations. Seaweed liquid also revealed the highest values of all traits in the absence of salt stress. Photosynthetic and biochemical traits without proline, Relative water content, and chlorophyll a/b declined more than other quality and growth traits with a rise in salt content from 0 to 40 mM. Further research will be needed to test the beneficial effects of seaweed liquid on traits of L. officinalis seedlings in outdoor landscaping that includes salty spaces.

Specificity landscapes unmask submaximal binding site preferences of transcription factors.

We have developed Differential Specificity and Energy Landscape (DiSEL) analysis to comprehensively compare DNA-protein interactomes (DPIs) obtained by high-throughput experimental platforms and cutting edge computational methods. While high-affinity DNA binding sites are identified by most methods, DiSEL uncovered nuanced sequence preferences displayed by homologous transcription factors. Pairwise analysis of 726 DPIs uncovered homolog-specific differences at moderate- to low-affinity binding sites (submaximal sites). DiSEL analysis of variants of 41 transcription factors revealed that many disease-causing mutations result in allele-specific changes in binding site preferences. We focused on a set of highly homologous factors that have different biological roles but "read" DNA using identical amino acid side chains. Rather than direct readout, our results indicate that DNA noncontacting side chains allosterically contribute to sculpt distinct sequence preferences among closely related members of transcription factor families.

The determinants of employability of people living with HIV/AIDS in Turkey.

BACKGROUND: This study addresses an important field within HIV research, the factors affecting the determinants of the employability of people living with HIV/AIDS (PLHIV) in Turkey. The employability of PLHIV is now even more vital because the use of antiretroviral therapy improves the quality of life of patients. In spite of this, the related literature suggests that there are serious impediments to the employment of PLHIV who face considerable levels of discrimination based on their HIV status. METHODS: This is a cohort study of 170 PLHIV of working age, treated at the Izmir Bozyaka Education and Training Hospital. We use a univariate logistic model to determine the effects of all determinants of interest with probit/logit modeling and penalized maximum likelihood estimation to avoid bias and to test the robustness of results. RESULTS: Age, time since diagnosis, work status at diagnosis, wealth status, illicit drug use, and CD4 cell count were significantly related to the employability of PLHIV. Younger individuals had a higher probability of workforce participation. HIV-infected patients aged 19 to 39 and 40 to 54 years were 32% and 20% more likely, respectively, to be employed. Economically better-off PLHIV were more likely to participate in the labor force and HIV patients who were working at the time of diagnosis were more likely to be re-employed. Time since diagnosis was negatively associated with the employment status. Compared to recently diagnosed patients, PLHIV for more than a decade were less likely to be employed. Those with high CD4 cell counts were more likely to be employed. Illicit drug use was negatively associated with employment and drug-addicted HIV patients were less likely to be employed. Higher education did not significantly predict the employability of PLHIV. CONCLUSIONS: Our results suggest that besides immunological status, socioeconomic factors play a substantial role in the employability of PLHIV. We suggest that even if a patient is skilled, educated, and qualified for the job, other factors such as stigma and employment discrimination in the workplace may hinder employment even among highly educated PLHIV.

The impact of economic and social factors on the prevalence of hepatitis B in Turkey.

BACKGROUND: Viral Hepatitis is one of the major global health problems, affecting millions of people every year. Limited information is available on the impact of social and economic factors on the prevalence of Hepatitis B virus (HBV) in Turkey. This study, contrary to other studies in the literature, was undertaken with the aim of examining the Majority of the excluded data come from the volunteers. METHODS: There are medical and the social-economic factors affecting the prevalence of HBV. This research, while taking medical factors as control variables, clarify the social and economic factors affecting the prevalence of HBV by utilising clinical data with the use of the Binary Probit Model (BPM). The BPM estimation is a powerful tool to determine not only the factors but explain also the exact impacts of each factor. RESULTS: The estimations of the BPM shows that economic and social variables such as age, gender, migration, education, awareness, social welfare, occupation are very important factors for determining HBV prevalence. Compared to the youngest population, the 46 to 66+ age group has a higher prevalence of HBV. The male respondents were 5% more likely to develop HBV compared to females. When region-specific differences are taken into account, migrating from the poorest parts of the country such as the eastern and south-eastern regions of Turkey are approximately 16% more likely to be infected. The welfare indicators such as a higher number of rooms in the respondent's house or flat decreases the probability of having HBV and, relatively higher income groups are less likely to develop HBV compared to labourers. The Self-employed/Business owner/Public sector worker category are approximately 10% less likely to develop HBV. When people are aware of the methods of prevention of HBV, they are 6% less likely to be infected. Previous HBV infection history increases the probability of having HBV again B by 17%. CONCLUSIONS: These findings strongly suggest that the impact of social and economic factors on the prevalence of HBV is vital. Any improvements in these factors are likely to reduce prevalence of HBV.

Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly.

The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report here that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility. Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. In addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.

The effect of sacral erector spinae plane block on the quality of recovery after total hip arthroplasty: a prospective, randomized, controlled, multicenter study.

BACKGROUND: Total hip arthroplasty, commonly performed to alleviate hip pain and enhance functionality in elderly patients, requires effective postoperative pain management to reduce opioid consumption and its associated side effects. A novel regional anaesthesia technique, the sacral erector spinae plane block, has the potential to enhance the quality of postoperative recovery significantly. METHODS: This prospective, randomized, controlled multicenter study investigated the effects of the sacral erector spinae plane block on recovery quality in patients undergoing total hip arthroplasty. The study comprised 50 patients, divided into Group S (patients receiving patients receiving sacral erector spinae plane block [S-ESPB]) and Group C (patients getting just multimodal analgesia). The primary outcome measured was the Quality of Recovery-15 score 24 hours post-surgery. Secondary outcomes included postoperative numerical rating scale scores (A score of 0 indicates no pain, while 10 indicates the most severe pain), total consumption of rescue analgesics, time to first rescue analgesic administration, patient satisfaction, time to first ambulation, the occurrence of complications, and the need for antiemetics. RESULTS: Group S had markedly higher quality of recovery-15 scores compared to Group C (Group S: median 117 percentiles [97-121]; Group C: median 89 percentiles [75-96]; P<0.001). Group S scored higher in postoperative pain, physical comfort, support, emotional state, and general quality of recovery-15 (P<0.001). Nevertheless, the physical independence category ratings were comparable across both groups (P=0.286). CONCLUSIONS: Sacral erector spinae plane block is a promising analgesic technique that enhances postoperative recovery and patient comfort in total hip arthroplasty.

Conformational control of the binding of the transactivation domain of the MLL protein and c-Myb to the KIX domain of CREB.

The KIX domain of CBP is a transcriptional coactivator. Concomitant binding to the activation domain of proto-oncogene protein c-Myb and the transactivation domain of the trithorax group protein mixed lineage leukemia (MLL) transcription factor lead to the biologically active ternary MLL∶KIX∶c-Myb complex which plays a role in Pol II-mediated transcription. The binding of the activation domain of MLL to KIX enhances c-Myb binding. Here we carried out molecular dynamics (MD) simulations for the MLL∶KIX∶c-Myb ternary complex, its binary components and KIX with the goal of providing a mechanistic explanation for the experimental observations. The dynamic behavior revealed that the MLL binding site is allosterically coupled to the c-Myb binding site. MLL binding redistributes the conformational ensemble of KIX, leading to higher populations of states which favor c-Myb binding. The key element in the allosteric communication pathways is the KIX loop, which acts as a control mechanism to enhance subsequent binding events. We tested this conclusion by in silico mutations of loop residues in the KIX∶MLL complex and by comparing wild type and mutant dynamics through MD simulations. The loop assumed MLL binding conformation similar to that observed in the KIX∶c-Myb state which disfavors the allosteric network. The coupling with c-Myb binding site faded, abolishing the positive cooperativity observed in the presence of MLL. Our major conclusion is that by eliciting a loop-mediated allosteric switch between the different states following the binding events, transcriptional activation can be regulated. The KIX system presents an example how nature makes use of conformational control in higher level regulation of transcriptional activity and thus cellular events.

Comparative Assessment of Outcomes in Drug Treatment for Smoking Cessation and Role of Genetic Polymorphisms of Human Nicotinic Acetylcholine Receptor Subunits.

Objective: To investigate the effects of genetic polymorphisms of human nicotinic acetylcholine receptor subunits α3, α4 and α5, which are encoded by CHRNA3, CHRNA4 CHRNA5 genes, respectively, on nicotine addiction and outcomes of pharmacological treatments for smoking cessation. Methods: A total of 143 smokers and 130 non-smokers were included. Genotyping for CHRNA3 rs578776, CHRNA4 rs1044396-rs1044397, CNRNA5 rs16969968 polymorphisms was performed by PCR, flowed by RFLP. Clinical outcomes and success rates of pharmacological treatments for smoking cessation with nicotine replacement therapy (NRT), bupropion or varenicline were determined at the 12th week of the treatment. Results: Overall, 52 out of 143 (36.4%) smokers who received pharmacotherapy were able to quit smoking. Success rates for smoking cessation were similar for female (30.3%) and male (41.6%) subjects (p = 0.16). The success rate for smoking cessation treatment with varenicline (58.5%) was significantly higher as compared to other treatments with NRT (20.0%), bupropion (32.3%) or bupropion + NRT (40.0%) (chi-square test, p = 0.001). Smoker vs. non-smoker status and the clinical outcomes of drugs used for smoking cessation were found similar in subjects carrying wild-type and variant alleles of human nicotinic acetylcholine receptor α subunits. Conclusion: In this study, smoking cessation treatment with varenicline was significantly more effective than treatments with nicotine replacement or bupropion in a cohort of Turkish subjects. Smoker/non-smoker status and the clinical outcomes of treatment with pharmacological agents were similar in subjects with wild-type or variant alleles for human nicotinic acetylcholine receptor subunits α3 (CHRNA3), α4 (CHRNA4) and α5 (CHRNA5).

Rapid drug desensitization with platin-based chemotherapy: Analysis of risk factors for breakthrough reactions.

BACKGROUND: All platin-based chemotherapeutics can cause hypersensitivity reactions (HSRs). With rapid drug desensitization (RDD), few patients experience breakthrough reactions (BTR) during desensitization. However, data about risk factors for BTRs during RDD in patients with HSRs to platins are limited. We first aimed to describe characteristics of our platin-reactive population and to validate the Brigham and Women's Hospital's (BWH's) RDD protocol in our population along with their outcomes with RDD. Our second aim was to identify the risk factors for BTRs. METHOD: This was a retrospective chart review (2013-2020) of patients with symptoms of immediate HSRs to platins. Initial HSRs were classified as grade 1, 2, or 3 based on their severity. Skin prick tests (SPT)/intradermal tests (IDT) were performed with implicated platins. A 12-step protocol was used during RDD. RESULTS: The study comprised 65 women and seven men (mean age 57.78 ± 8.73 years). Initial HSRs to carboplatin, cisplatin, and oxaliplatin occurred in 38, 13, and 21 patients, respectively. All patients reacted at the fifth (median) recurrent infusions (min:1, max:20). The median values for carboplatin, cisplatin, and oxaliplatin were 6 (1-20), 3 (1-15), and 3 (1-11), respectively. Most initial HSRs were grade 2 (n = 40, 55.6%) and 3 (n = 27, 37.5%); only 6.9% (n = 5) were grade 1. Patients with grade 1, 2, and 3 initial HSRs had positive platin skin test results at rates of 80%, 74%, and 88%, respectively.A total of 232 RDDs were performed in 72 patients and 98.7% of these desensitizations were completed. BTRs occurred in 56 (24.1%) (grade 1 n = 14, 25%; grade 2 n = 32, 57%; grade 3 n = 10, 18%) of these desensitizations. Breakthrough reactions were more severe in patients with positive SPTs or 1:100 or 1:10 dilutions of IDT (p = 0.014). BTR was not observed during RDD in any of the patients with positive 1:1 dilutions of IDT. Positivity on prick or 1:100 or 1:10 IDT increased the risk of BTR 5.058 times. There was no significant association between the risk of BTRs and age, drug cycle, sex, comorbidities, or atopy. CONCLUSION: In our experience, 98.7% of 232 RDDs to platins were completed successfully, showing that RDD was safe and effective. Drug skin test positivity is a potential marker for identifying high-risk patients who will have BTRs during RDDs to platins.

Performance of pulmonary embolism severity index in predicting long-term mortality after acute pulmonary embolism.

OBJECTIVE: In this study, we aimed to evaluate the accuracy of the original and simplified pulmonary embolism (PE) severity index (PESI) to predict all-cause mortality after 30 days of acute PE diagnosis up to five years within consecutive sub-periods. METHODS: Adult patients diagnosed with acute PE between January 1, 2003, and June 30, 2013, were retrospectively included. Data on baseline characteristics and mortality during a five-year follow-up were collected. RESULTS: The study included 414 patients (Male/Female=192/222). The median age at diagnosis was 61.5 (minimum-maximum, 18-93) years. Mortality rates were 13.3% at 30 days, 21.8% at 90 days, 32.6% at one year, and 51.0% at five years. Both stratification into risk classes according to the original PESI and low vs. high-risk classification of original and simplified PESI were significantly correlated with the 30-day, 31-90-day, 91-day-one-year, and one-five-year mortality. Significant PESI predictors for mortality were history of cancer [hazard ratio (HR): 3.31, 95% confidence interval (CI): 1.64-6.68; p=0.001] and heart failure (HR: 2.35, 95% CI: 1.04-5.32, p=0.041) at 31-90-day, history of cancer (HR: 5.45, 95% CI: 2.86-10.40, p<0.001) at 91-day-one-year, advancing age (HR: 1.04, 95% CI: 1.02-1.06, p<0.001) and history of cancer (HR: 5.53, 95% CI: 3.41-8.98, p<0.001) at one-five-year after acute PE diagnosis. CONCLUSION: All-cause long-term mortality in high-risk patients with acute PE according to original or simplified PESI significantly increased up to five years of follow-up. This survival disadvantage was mainly related to cancer and comorbidities rather than acute clinical manifestations. Future prospective studies are needed to demonstrate the effect of various comorbidities on long-term mortality in these patients.

Cross-Sectional Analysis of Prevalence and Aetiological Factors of Dental Erosion in Turkish Children Aged 7-14 Years.

PURPOSE: This study aimed to estimate the prevalence, distribution, and the associated factors of tooth erosion in Turkish school children. MATERIALS AND METHODS: A cross-sectional analysis was performed on a representative sample of 473 children (aged 7-14 years) from 11 public schools in Turkey. Parents were asked to fill out a questionnaire to collect sociodemographic data. A questionnaire was also given to the children, to collect data pertaining to personal demographic details and habits of consuming acidic foods and drinks. The O'Sullivan index was used to assess affected permanent teeth. The data were analysed using a chi-square test and multivariate logistic regression analysis. RESULTS: Dental erosion was observed in 21.8% of the children. Lesions were most often observed in the enamel with less than half of the buccal surface affected. Erosion was found to be statistically significantly higher in older children and in those with an elevated body mass index (BMI) (p <0.05). The consumption of fruit juices, drinks with cola, orange soft drinks, gaseous, cocoa milk, iced tea, sodas, sports drinks, energy drinks, oranges, lemons, kiwis, grapefruits, apples, peaches, and fruit yogurts was statistically significantly higher in students with erosion (p <0.05). There was no statistically significant relationship between students' sex, systemic disease, premature birth and low birth weight, exercise activity level, socioeconomic status, parental education level, and oral hygiene habits with erosion (p >0.05). CONCLUSION: Although erosive lesions were limited to the enamel, the prevalence of erosion was high. Erosion was statistically significantly associated with older age, elevated BMI, consumption of certain beverages, and fruit.

Effects of Genetic Polymorphisms of Drug Transporter ABCB1 (MDR1) and Cytochrome P450 Enzymes CYP2A6, CYP2B6 on Nicotine Addiction and Smoking Cessation.

OBJECTIVES: To determine the effects of genetic polymorphisms of ABCB1 (MDR1), CYP2A6, CYP2B6 on smoking status, and clinical outcomes of smoking cessation therapies in a Turkish population. METHODS: 130 smokers and 130 non-smokers were recruited. Individuals who never smoked were described as non-smokers. 130 smokers were treated with nicotine replacement therapy (NRT) (n = 40), bupropion (n = 47), bupropion + NRT (n = 15), and varenicline (n = 28). Smokers were checked by phone after 12 weeks of treatment whether they were able to quit smoking or not. Genotyping and phenotyping were performed. RESULTS: Cessation rates were as follows; 20.0% for NRT, 29.8% for bupropion, 40.0% for bupropion + NRT, 57.1% for varenicline (p = 0.013). The frequency of ABCB1 1236TT-2677TT-3435TT haplotype was significantly higher in non-smokers as compared to smokers (21.5% vs. 10.8, respectively; p = 0.018). Neither smoking status nor smoking cessation rates were associated with genetic variants of CYP2A6 (p = 0.652, p = 0.328, respectively), or variants of CYP2B6 (p = 0.514, p = 0.779, respectively). CONCLUSION: Genetic variants of the drug transporter ABCB1 and the 1236TT-2677TT-3435TT haplotype was significantly associated with non-smoking status. Neither ABCB1 nor CYP2A6, CYP2B6 genetic variants were associated with smoking cessation rates at the 12th week of drug treatment.

Triple test with tumor markers CYFRA 21.1, HE4, and ProGRP might contribute to diagnosis and subtyping of lung cancer.

BACKGROUND AND AIM: Early diagnosis and histological subtyping are important issues in the management of patients with lung cancer (LC). The aim of this study is to investigate the diagnostic value of a panel of serum tumor markers in newly diagnosed patients with LC. METHODS: Venous blood samples were collected from 99 patients with LC (42 adenocarcinoma, 35 squamous, and 22 small cell carcinoma) and 30 patients with benign lung disease. Progastrin releasing peptide (ProGRP), squamous cell carcinoma antigen (SCCAg), cytokeratin 19-fragments (CYFRA 21.1), human epididymis protein 4 (HE4), Chromogranin A (CgA) and neuron specific enolase (NSE) levels were measured. The diagnostic value of the biomarkers was assessed with ROC curve analyses; the area under the curve (AUC) was calculated. RESULTS: Serum CYFRA 21.1, ProGRP, SCCAg, NSE levels were significantly higher in LC patients. While ProGRP levels were higher (p = 0.009) in SCLC; CYFRA 21.1 and SCCAg levels were higher in NSCLC (p = 0.019 and p = 0.001, respectively). The sensitivity and specificity of tumor markers were 72%, 83% for CYFRA 21.1; 70%, 57% for HE4; 18%, 93% for ProGRP; 43%, 77% for SCCAg; 54%, 53% for CgA; 73%, 50% for NSE. CYFRA 21.1 (p < 0.001, r = 0.394), HE4 (p = 0.014, r = 0.279) and CgA (p = 0.023, r = 0.259) levels were positively correlated with tumor stage in NSCLC. CgA levels were significantly higher in extensive stage SCLC (p = 0.004). CYFRA 21.1 had the highest diagnostic value for LC (AUC = 0.865). When it is combined with HE4, diagnostic value increased (AUC = 0.899). ProGRP had the highest diagnostic value (AUC = 0.875, p < 0.001) for discriminating SCLC from NSCLC. CONCLUSION: A panel of three tumor markers CYFRA 21.1, HE4 and ProGRP may play a role for discriminating LC from benign lung disease and subtyping as SCLC.

Interplay of Electrostatics and Hydrophobic Effects in the Metamorphic Protein Human Lymphotactin.

The human lymphotactin (hLtn) is a protein that features two native states both of which are physiologically relevant: it is a monomer (hLtn10) at 10 °C with 200 mM salt and a dimer (hLtn40) at 40 °C and without salt. Here we focus on the networks of electrostatic and hydrophobic interactions that display substantial changes upon the conversion from hLtn10 to hLtn40 since they are expected to modulate the relative stability of the two folds. In addition to the Arg 23-Arg 43 interaction discussed in previous work, we find several other like-charge pairs that are likely important to the stability of hLtn10. Free energy perturbation calculations are carried out to explicitly evaluate the contribution of the Arg 23-Arg 43 interaction to the hLtn10 stability. hLtn40 features a larger number of salt bridges, and a set of hydrophobic residues undergo major changes in the solvent accessible surface area between hLtn10 and hLtn40, pointing to their importance to the relative stability of the two folds. We also discuss the use of explicit and implicit solvent simulations for characterizing the conformational ensembles under different solution conditions.

Identification of the Ah-receptor structural determinants for ligand preferences.

The aryl hydrocarbon receptor (AHR) is a transcription factor that responds to diverse ligands and plays a critical role in toxicology, immune function, and cardiovascular physiology. The structural basis of the AHR for ligand promiscuity and preferences is critical for understanding AHR function. Based on the structure of a closely related protein HIF2α, we modeled the AHR ligand binding domain (LBD) bound to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and benzo(a)pyrene (BaP) and identified residues that control ligand preferences by shape and H-bond potential. Mutations to these residues, particularly Q377 and G298, resulted in robust and opposite changes in the potency of TCDD and BaP and up to a 20-fold change in the ratio of TCDD/BaP efficacy. The model also revealed a flexible "belt" structure; molecular dynamic (MD) simulation suggested that the "belt" and several other structural elements in the AHR-LBD are more flexible than HIF2α and likely contribute to ligand promiscuity. Molecular docking of TCDD congeners to a model of human AHR-LBD ranks their binding affinity similar to experimental ranking of their toxicity. Our study reveals key structural basis for prediction of toxicity and understanding the AHR signaling through diverse ligands.