Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis.

Protein degradation plays important roles in biological processes and is tightly regulated. Further, targeted proteolysis is an emerging research tool and therapeutic strategy. However, proteome-wide technologies to investigate the causes and consequences of protein degradation in biological systems are lacking. We developed "multiplexed proteome dynamics profiling" (mPDP), a mass-spectrometry-based approach combining dynamic-SILAC labeling with isobaric mass tagging for multiplexed analysis of protein degradation and synthesis. In three proof-of-concept studies, we uncover different responses induced by the bromodomain inhibitor JQ1 versus a JQ1 proteolysis targeting chimera; we elucidate distinct modes of action of estrogen receptor modulators; and we comprehensively classify HSP90 clients based on their requirement for HSP90 constitutively or during synthesis, demonstrating that constitutive HSP90 clients have lower thermal stability than non-clients, have higher affinity for the chaperone, vary between cell types, and change upon external stimuli. These findings highlight the potential of mPDP to identify dynamically controlled degradation mechanisms in cellular systems.

Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition.

Complex disease phenotypes often span multiple molecular processes. Functional characterization of these processes can shed light on disease mechanisms and drug effects. Thermal Proteome Profiling (TPP) is a mass-spectrometry (MS) based technique assessing changes in thermal protein stability that can serve as proxies of functional protein changes. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a multi-omics integration framework, to provide an integrated view of transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover consequences of Poly (ADP-ribose) polymerase (PARP) inhibition in ovarian cancer cells on cell cycle and DNA damage response as well as interferon and hippo signaling. We found that TPP offers a complementary perspective to other omics data modalities, and that its integration allowed us to obtain a more complete molecular overview of PARP inhibition. We anticipate that this strategy can be used to integrate functional proteomics with other omics to study molecular processes.

The use of respiratory muscle training in patients with pulmonary dysfunction, internal diseases or central nervous system disorders: a systematic review with meta-analysis.

OBJECTIVE: The aim of this systematic review with meta-analysis was to evaluate the effectiveness of RMT in internal and central nervous system disorders, on pulmonary function, exercise capacity and quality of life. METHODS: The inclusion criteria were (1) publications designed as Randomized Controlled Trial (RCT), with (2) participants being adults with pulmonary dysfunction caused by an internal disease or central nervous system disorder, (3) an intervention defined as RMT (either IMT or EMT) and (4) with the assessment of exercise capacity, respiratory function and quality of life. For the methodological quality assessment of risk of bias, likewise statistical analysis and meta-analysis the RevMan version 5.3 software and the Cochrane Risk of Bias Tool were used. Two authors independently analysed the following databases for relevant research articles: PubMed, Scopus, Cochrane Library, Web of Science, and Embase. RESULTS: From a total of 2200 records, the systematic review includes 29 RCT with an overall sample size of 1155 patients. Results suggest that patients with internal and central nervous system disorders who underwent RMT had better quality of life and improved significantly their performance in exercise capacity and in respiratory function assessed with FVC and MIP when compared to control conditions (i.e. no intervention, sham training, placebo or conventional treatments). CONCLUSION: Respiratory muscle training seems to be more effective than control conditions (i.e. no intervention, sham training, placebo or conventional treatment), in patients with pulmonary dysfunction due to internal and central nervous system disorders, for quality of life, exercise capacity and respiratory function assessed with MIP and FVC, but not with FEV1.

Synthesis and Evaluation of Novel Ring-Strained Noncanonical Amino Acids for Residue-Specific Bioorthogonal Reactions in Living Cells.

Bioorthogonal reactions are ideally suited to selectively modify proteins in complex environments, even in vivo. Kinetics and product stability of these reactions are crucial parameters to evaluate their usefulness for specific applications. Strain promoted inverse electron demand Diels-Alder cycloadditions (SPIEDAC) between tetrazines and strained alkenes or alkynes are particularly popular, as they allow ultrafast labeling inside cells. In combination with genetic code expansion (GCE)-a method that allows to incorporate noncanonical amino acids (ncAAs) site-specifically into proteins in vivo. These reactions enable residue-specific fluorophore attachment to proteins in living mammalian cells. Several SPIEDAC capable ncAAs have been presented and studied under diverse conditions, revealing different instabilities ranging from educt decomposition to product loss due to ß-elimination. To identify which compounds yield the best labeling inside living mammalian cells has frequently been difficult. In this study we present a) the synthesis of four new SPIEDAC reactive ncAAs that cannot undergo ß-elimination and b) a fluorescence flow cytometry based FRET-assay to measure reaction kinetics inside living cells. Our results, which at first sight can be seen conflicting with some other studies, capture GCE-specific experimental conditions, such as long-term exposure of the ring-strained ncAA to living cells, that are not taken into account in other assays.

Monitoring Physical Activity with a Wearable Sensor in Patients with COPD during In-Hospital Pulmonary Rehabilitation Program: A Pilot Study.

Accelerometers have become a standard method of monitoring physical activity in everyday life by measuring acceleration in one, two, or three axes. These devices provide reliable and objective measurements of the duration and intensity of physical activity. We aimed to investigate whether patients undertake physical activity during non-supervised days during stationary rehabilitation and whether patients adhere to the rigor of 24 h monitoring. The second objective was to analyze the strengths and weaknesses of such kinds of sensors. The research enrolled 13 randomly selected patients, qualified for in-patient, 3 week, high-intensity, 5 times a week pulmonary rehabilitation. The SenseWear armband was used for the assessment of physical activity. Participants wore the device 24 h a day for the next 4 days (Friday-Monday). The analysis of the number of steps per day, the time spent lying as well as undertaking moderate or vigorous physical activity (>3 metabolic equivalents of task (METs)), and the energy expenditure expressed in kcal showed no statistically significant difference between the training days and the days off. It seems beneficial to use available physical activity sensors in patients with chronic obstructive pulmonary disease (COPD); measurable parameters provide feedback that may increase the patient's motivation to be active to achieve health benefits.

Prehospital pain management in children with traumatic injuries.

UNLABELLED: Damage that arises as a result of injuries is one of the most common causes of children presenting to hospital emergency departments. OBJECTIVES: The aim of the study was to assess the implementation of recommendations for prehospital pain management in injured children provided by various health care centers. METHODS: A total of 7146 children aged 0 to 18 years because of injury were admitted to the Department of Paediatric Emergency Medicine in the Maria Konopnicka Memorial University Teaching Hospital No. 4 in Lodz within the period of 12 months. From this group, 1493 children received prehospital emergency care from various health care centers. RESULTS: Health care centers provided prehospital aid to 21% of all children with injuries. Boys (60.3%) and children older than 5 years (80%) predominated among pediatric trauma cases. Prehospital emergency aid was most frequently administered to children by emergency medical services personnel (42.7%) and a primary health care physician (28.1%). Injuries of head (42.1%), neck (1.1%), chest (1.7%), abdomen (2.5%), upper (32.2%), and lower (19.9%) limbs as well as burns (5.3%) were diagnosed in pediatric patients. Indications for prehospital analgesia were found in 489 of 1493 patients (32.7%). Analgesia was administered to 159 children (32%), pain medication was not given to 223 children (46%), and in 107 cases (22%), there was a lack of information on that subject. CONCLUSIONS: Despite the training of medical staff, provision of analgesia for children with burns and traumatic injuries of the osteoarticular system is inadequate.

Condensin: crafting the chromosome landscape.

The successful transmission of complete genomes from mother to daughter cells during cell divisions requires the structural re-organization of chromosomes into individualized and compact structures that can be segregated by mitotic spindle microtubules. Multi-subunit protein complexes named condensins play a central part in this chromosome condensation process, but the mechanisms behind their actions are still poorly understood. An increasing body of evidence suggests that, in addition to their role in shaping mitotic chromosomes, condensin complexes have also important functions in directing the three-dimensional arrangement of chromatin fibers within the interphase nucleus. To fulfill their different functions in genome organization, the activity of condensin complexes and their localization on chromosomes need to be strictly controlled. In this review article, we outline the regulation of condensin function by phosphorylation and other posttranslational modifications at different stages of the cell cycle. We furthermore discuss how these regulatory mechanisms are used to control condensin binding to specific chromosome domains and present a comprehensive overview of condensin's interaction partners in these processes.

T-CrAsH: a heterologous chemical crosslinker.

Copper-free click chemistry is currently the most promising and most rapidly developing technology for performing tailored chemical reactions inside intact living cells and animals. Its potential is particularly intensely explored in the field of live cell imaging, for both proteins and metabolites. Here we expand the application spectrum of click reactions to the chemical crosslinking of two proteins of choice in living cells. By combining strain-promoted Diels-Alder cycloaddition with FlAsH-based labeling of peptidic tetracysteine motifs, we developed the membrane-permeating reversible crosslinker T-CrAsH. We demonstrate the feasibility of the method both in vitro and inside cells. The biggest advantage of this new tool is the small size of the crosslinkable groups; this significantly decreases the risk of functional interference.

A rapidly reversible chemical dimerizer system to study lipid signaling in living cells.

Chemical dimerizers are powerful tools for non-invasive manipulation of enzyme activities in intact cells. Here we introduce the first rapidly reversible small-molecule-based dimerization system and demonstrate a sufficiently fast switch-off to determine kinetics of lipid metabolizing enzymes in living cells. We applied this new method to induce and stop phosphatidylinositol 3-kinase (PI3K) activity, allowing us to quantitatively measure the turnover of phosphatidylinositol 3,4,5-trisphosphate (PIP3) and its downstream effectors by confocal fluorescence microscopy as well as standard biochemical methods.

Synergistic effects of PARP inhibition and cholesterol biosynthesis pathway modulation.

An in-depth multi-omic molecular characterisation of poly(adenosine 5'-diphosphate [ADP]-ribose) polymerase (PARP) inhibitors revealed a distinct poly-pharmacology of niraparib (Zejula®) mediated by its interaction with lanosterol synthase (LSS), which is not observed with other PARP inhibitors. Niraparib, in a similar way to the LSS inhibitor Ro-48-8071, induced activation of the 24,25-epoxysterol shunt pathway, which is a regulatory signalling branch of the cholesterol biosynthesis pathway. Interestingly, the combination of a LSS inhibitor with a PARP inhibitor that does not bind to LSS, such as olaparib, had an additive effect on killing of cancer cells to levels comparable to Niraparib as single agent. In addition, the combination of PARP inhibitors and statins, inhibitors of HMGCR, an enzyme catalysing the rate-limiting step in the mevalonate pathway, had a synergistic effect on tumor cell killing in cell lines and patient-derived ovarian tumor organoids. These observations suggest that concomitant inhibition of cholesterol biosynthesis pathway and PARP activity might result in stronger efficacy of these inhibitors against tumor types highly dependent on cholesterol metabolism.

Inpatient post-COVID-19 rehabilitation program featuring virtual reality-Preliminary results of randomized controlled trial.

Background: Numerous recommendations from pulmonary scientific societies indicate the need to implement rehabilitation programs for patients after COVID-19. The aim of this study was to propose an innovative comprehensive intervention based on a hospital-based pulmonary rehabilitation program for individuals with post-acute sequelae of COVID-19. Methods: It was decided to evaluate two forms of hospital rehabilitation: traditional and one provided through virtual reality. Preliminary results are based on a group of 32 patients (20 female and 12 male), of average age 57.8 (4.92) years in the period of 3-6 months after the initial infection. Primary outcomes included analysis of lung function, exercise performance and stress level. A 3-week, high-intensity, five-times per week pulmonary rehabilitation program was designed to compare the effectiveness of a traditional form with a VR-led, novel form of therapy. Results: The analysis of the results showed a statistically significant improvement in both groups with regard to exercise performance expressed as 6MWT distance. Moreover, a statistically significant decrease in dyspnoea levels following the 6MWT was also noted in intergroup comparison, but the between-group comparison revealed non-statistically significant changes with low effect size. Regarding lung function, the analysis showed essentially normal lung function at baseline and a non-statistically significant improvement after the completion of the rehabilitation program. The analysis of the stress level showed a statistically significant improvement in both groups within the inter-group comparison, yet the between-group comparison of deltas values showed a non-significant difference with low effect size. Conclusion: A 3-weeks inpatients pulmonary rehabilitation program led to improvement of the exercise performance of people with post-acute sequelae of COVID-19, but not lung function. Furthermore, the program was shown to reduce patients' stress levels. A comparison of the traditional form of rehabilitation to the novel form using VR, shows similar effectiveness in terms of exercise performance and stress levels.

Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.

Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome-nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors.

Protein tango: the toolbox to capture interacting partners.

The evaluation of protein function in the context of the whole cell is crucial for understanding of living systems. In this context, the identification and modulation of protein-protein interactions in and outside cells is of ample importance. Several methods have been developed in the past years to detect and/or actively induce protein-protein interactions in living cells. As a result, tools are now available to manipulate intracellular events by reversible or irreversible cross-linking of proteins in a specific manner. These techniques open many new doors and enable the dissection of complicated protein networks. Herein we describe which cross-linkers and inducers of dimerization are out there and how to make use of this great toolbox.

Remote Interventions to Support Students' Psychological Well-Being during the COVID-19 Pandemic: A Narrative Review of Recent Approaches.

The COVID-19 pandemic has negatively affected students' mental health, and it is important to implement mental health management strategies. The purpose of this study was to present current findings on the implementation of remote mental health interventions in students during the pandemic. The PubMed and Web of Science electronic databases were searched and, from a total of 174 articles, 106 records were excluded according to the inclusion criteria and 23 were assessed as full texts. After the full-text screening, 12 studies were included in the review. The included publications were randomized clinical trials focused on remote mental support interventions among students from 10 countries, representing both genders, and were in the average age range of 17-55 years with an overall number of 892 participants. The included studies covered the effectiveness of strictly psychotherapeutic programs, such as cognitive-behavioral therapy (CBT) and dialectical behavior therapy (DBT), as well as other techniques such as mindfulness, laughter therapy, the brain wave modulation technique (BWM-T), and physical activity-based interventions. This narrative review provides an overview of studies with a wide range of types of remote mental health support interventions. Each of the forms of intervention analyzed in this review resulted in positive changes in students' mental health, which indicates hope for widespread help via various forms of intervention implemented remotely.

Telemedicine Interventions as an Attempt to Improve the Mental Health of Populations during the COVID-19 Pandemic-A Narrative Review.

Published reports indicate the need for psychological interventions and the integration of psychiatric care into crisis management plans in people with mental health issues caused by the COVID-19 pandemic. It seems crucial to identify the root causes of the health-social-economic crisis and identify potential opportunities for widely implemented psychological assistance. This narrative literature review aims to identify the types of interventions deployed as telemedicine-based mental health support and their effectiveness. The PubMed and Web of Science electronic databases were searched. From a total of 48 articles, 46 were analysed after removing duplicates. From these, thirty-seven records were excluded according to the inclusion criteria and nine (eight RCT and one cross-over) were assessed as full texts. The included publications were randomised clinical trials or cross-over studies focused on remote mental support interventions. In all studies, participants represented both sexes and had an average age range of 6-64. Studies included participants from seven countries and the overall number of participants in the included studies was 687. The content of these intervention programmes includes both established psychotherapeutic programmes, as well as new interventions. Remote support was implemented through three approaches: phone/video calls, mobile applications, and internet-based programs. The results of the included studies indicate a higher or equal efficacy of telemedicine interventions compared to traditional forms. The review also revealed a relatively wide range of targeted research groups: from children with social anxiety through to their caregivers; adolescents with neurological disorders; and from college students to adults with psychiatric or orthopaedic disorders. Analysis of the included papers found that telemedicine interventions show promising results as an attempt to improve population mental health during the COVID-19 pandemic.

Use of Virtual Reality-Based Therapy in Patients with Urinary Incontinence: A Systematic Review with Meta-Analysis.

It is estimated that over 400 million people worldwide experience some form of urinary incontinence (UI). Pelvic floor muscle training (PFMT) is commonly used in cases of urine loss. Game therapy (GT) has been suggested as a new conservative modality for UI treatments. GT represents a form of virtual reality (VR) that allows users to interact with elements of a simulated scenario. The purpose of this review was to assess the potential of using VR-based PFMT in the treatment of UI with a particular focus on the impact of this form of therapy on the patients' muscle function, symptoms of UI and quality of life (QoL). The following electronic databases were searched: PubMed, Embase, Cochrane Library, Scopus and Web of Science. Systematic review methods were based on the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) statement. Electronic medical databases were searched from inception to 28 January 2021. From a total of 38 articles, 26 were analyzed after removing duplicates, then 22 records were excluded according to inclusion criteria and 4 were assessed as full texts. Finally, 2 randomized controlled trials (RCT) with 79 patients were included. For the International Consultation on Incontinence Questionnaire-Short Form (ICIQ-SF), the meta-analysis showed a significant difference in favor of the control condition (MD = 2.22; 95% CI 0.42, 4.01; I2 = 0%). Despite the popularity of the use of VR in rehabilitation, we found a scarcity of literature evaluating the application of VR in the field of UI therapy. Only one study matched all of the criteria established. The effects of VR training improved PFM function and QoL; however, these changes were comparable to those of traditional PFMT. It is not possible to reach final conclusions from one study; thus, further development of VR interventions in the field of UI treatments are needed.

Mental Health Conditions Among E-Learning Students During the COVID-19 Pandemic.

Aim: The COVID-19 pandemic has forced the education system to undergo changes, which have also affected universities. E-learning became the main form of education, reducing interpersonal contacts, which could affect the mental wellbeing of students. The aim of this study was to investigate the prevalence of depressive symptoms and the level of perceived stress during e-learning among Polish students and to identify the factors for predicting higher levels of depression symptoms. Methods: The study included 753 participants with a mean age of 22.47 (±4.02) years. The Perception of Stress Questionnaire (PSQ) and Beck Depression Inventory (BDI-II) were used to measure the severity of stress and level of depression. Furthermore, our own survey was used to assess the impact of e-learning on various aspects of life. To examine how much stress can explain a statistically significant amount of variance in depression, three-step hierarchical multiple regression was used. In addition, our own questionnaire was used to assess the impact of e-learning on education, social contacts and technical abilities. Results: A total of 58% of the students characterized by an increased level of stress. 56% show symptoms of depression and 18% of the participants had suicidal thoughts. The most significant predictor of depression is high stress levels and factors related to e-learning: isolation from friends and acquaintances, negative impact on level of knowledge, reduced motivation to learn, and worsening grades. This predictors may explain about 66% of the variance of depression. Conclusion: Universities should implement interventions and educational programmes, providing ad hoc assistance in the form of individual or group meetings with a psychologist (also in a remote form) and organizing workshops and webinars on strategies for managing stress.

Effects of a Short-Term Slackline Training Program on Energy Expenditure and Balance in Healthy Young Adults: A Preliminary Report of a Randomized Controlled Trial.

The development of technology and a fast-paced lifestyle has caused a significant decrease in physical activity, especially among young people. These worrying trends can be countered by the use of attractive forms of physical recreation, including the increasingly popular slackline. The aim of this study was to evaluate energy expenditure during slackline training and to analyze changes in dynamic and static balance parameters after supervised slackline training sessions. The study enrolled 28 healthy volunteers (14 men and 14 women aged 21−25) who were randomly divided into two groups: experimental and passive control. The energy expenditure level was the primary outcome and was assessed using the SenseWear Armband. Each participant underwent an initial and final balance assessment using two selected protocols on the Balance Master platform. The intervention lasted 5 days, with 15 min of supervised training per day. The average energy expenditure expressed in MET was 6.0 (±0.7) MET per training session. An analysis of the results regarding static and dynamic balance showed that the group participating in slackline training significantly improved stability on foam surfaces with their eyes open (p < 0.003), as well as tandem walk speeds (p < 0.05), both with small effect sizes. The results suggested that slackline training has the potential to produce significant positive effects on general health statuses following the World Health Organization's (WHO) recommendations on physical activity. The significant improvement in task-specific balance suggests that slackline training could become an important element of the prevention and rehabilitation of many injuries.

Effectiveness of an Inpatient Virtual Reality-Based Pulmonary Rehabilitation Program among COVID-19 Patients on Symptoms of Anxiety, Depression and Quality of Life: Preliminary Results from a Randomized Controlled Trial.

Forms of rehabilitation for patients after COVID-19 are gaining interest. The purpose of this study was to investigate and compare an innovative in-hospital pulmonary rehabilitation programs augmented with training elements performed in virtual reality. This randomized controlled study included 32 patients enrolled in post-COVID-19 rehabilitation at a Public Hospital in Poland. The rehabilitation models included exercise capacity training on a cycle ergometer, breathing and general fitness workout, resistance training, and relaxation. The forms of training and relaxation differed between the groups: the experimental group employed virtual reality, and the control group used a traditional form of therapy. Exercise tolerance was assessed using a 6 min walk test (6 MWT), while psychological parameters were evaluated using the Hospital Anxiety and Depression Scale (HADS) and the brief World Health Organization Quality of Life Scale (WHOQOL-BRIEF). The analysis of the post-rehabilitation results showed a statistically significant improvement in both groups regarding depression (VR: 6.9 (3.9) vs. 4.7 (3.5), p = 0.008; CG: 7.64 (4.5) vs. 6.6 (4.8), p = 0.017) and anxiety (VR: 8.6 (4.6) vs. 5.6 (3.3), p < 0.001; CG: 9.57 (6.0) vs. 8 (4.8), p = 0.003). No statistically significant improvements in quality of life were noted in both groups. Moreover, the analysis showed a statistically significant improvement in the exercise capacity in both groups after completion of the rehabilitation program, expressed as a distance in the 6 MWT, as well as a statistically significant improvement in dyspnea in the VR group. To conclude, the analysis of the preliminary data revealed that a 3-week hospital-based pulmonary rehabilitation program for COVID-19 patients led to an improvement in exercise tolerance as well as a reduction in the symptoms of anxiety and depression. The virtual reality-based form of training delivery, despite its attractiveness, did not significantly affect patients' performance.

A FlAsH-based cross-linker to study protein interactions in living cells.

As you like it: xCrAsH, a dimeric derivative of the arsenical compound FlAsH, enables the highly specific, covalent cross-linking of two proteins containing a 12 amino acid peptide tag. This inducible and (by addition of dithiols) reversible system can be used to detect and manipulate protein-protein interactions both in vitro and in living cells (see picture).