Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-specific Redox Proteomics*

Reversible protein thiol oxidation is an essential regulatory mechanism of photosynthesis, metabolism, and gene expression in photosynthetic organisms. Herein, we present proteome-wide quantitative and site-specific profiling of in vivo thiol oxidation modulated by light/dark in the cyanobacterium Synechocystis sp. PCC 6803, an oxygenic photosynthetic prokaryote, using a resin-assisted thiol enrichment approach. Our proteomic approach integrates resin-assisted enrichment with isobaric tandem mass tag labeling to enable site-specific and quantitative measurements of reversibly oxidized thiols. The redox dynamics of ∼2,100 Cys-sites from 1,060 proteins under light, dark, and 3-(3,4-dichlorophenyl)-1,1-dimethylurea (a photosystem II inhibitor) conditions were quantified. In addition to relative quantification, the stoichiometry or percentage of oxidation (reversibly oxidized/total thiols) for ∼1,350 Cys-sites was also quantified. The overall results revealed broad changes in thiol oxidation in many key biological processes, including photosynthetic electron transport, carbon fixation, and glycolysis. Moreover, the redox sensitivity along with the stoichiometric data enabled prediction of potential functional Cys-sites for proteins of interest. The functional significance of redox-sensitive Cys-sites in NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, peroxiredoxin (AhpC/TSA family protein Sll1621), and glucose 6-phosphate dehydrogenase was further confirmed with site-specific mutagenesis and biochemical studies. Together, our findings provide significant insights into the broad redox regulation of photosynthetic organisms.
ARABIDOPSIS : A RICH HARVEST 10 YEARS AFTER COMPLETION OF THE GENOME SEQUENCE Embryogenesis – the humble beginnings of plant life

Each plant starts life from the zygote formed by the fusion of an egg and a sperm cell. The zygote gives rise to a multicellular embryo that displays a basic plant body organization and is surrounded by nutritive endosperm and maternal tissue. How the body organization is generated had already been studied before the genome sequence of Arabidopsis thaliana was completed 10 years ago, but several regulatory mechanisms of embryo development have since been discovered or analysed in more detail. Although this progress did not strictly depend on the availability of the genome sequence itself, several advances were considerably facilitated. In this review, we mainly address early embryo development, highlighting general mechanisms and crucial regulators, including phytohormones, that are involved in patterning the embryo and were mainly analysed in the post-genome decade. We also highlight some unsolved problems, provide a brief outlook on the future of Arabidopsis embryo research, and discuss how the knowledge gained from Arabidopsis could be translated to crop species.
Systematically Ranking the Tightness of Membrane Association for Peripheral Membrane Proteins (PMPs)*

Large-scale quantitative evaluation of the tightness of membrane association for nontransmembrane proteins is important for identifying true peripheral membrane proteins with functional significance. Herein, we simultaneously ranked more than 1000 proteins of the photosynthetic model organism Synechocystis sp. PCC 6803 for their relative tightness of membrane association using a proteomic approach. Using multiple precisely ranked and experimentally verified peripheral subunits of photosynthetic protein complexes as the landmarks, we found that proteins involved in two-component signal transduction systems and transporters are overall tightly associated with the membranes, whereas the associations of ribosomal proteins are much weaker. Moreover, we found that hypothetical proteins containing the same domains generally have similar tightness. This work provided a global view of the structural organization of the membrane proteome with respect to divergent functions, and built the foundation for future investigation of the dynamic membrane proteome reorganization in response to different environmental or internal stimuli.
Cost-effectiveness Analysis of Nutritional Support for the Prevention of Pressure Ulcers in High-Risk Hospitalized Patients

OBJECTIVE:To evaluate the cost-effectiveness of nutritional support compared with standard care in preventing pressure ulcers (PrUs) in high-risk hospitalized patients. DESIGN:An economic model using data from a systematic literature review. A meta-analysis of randomized controlled trials on the efficacy of nutritional support in reducing the incidence of PrUs was conducted. PATIENTS:Modeled cohort of hospitalized patients at high risk of developing PrUs and malnutrition simulated during their hospital stay and up to 1 year. INTERVENTIONS:Standard care included PrU prevention strategies, such as redistribution surfaces, repositioning, and skin protection strategies, along with standard hospital diet. In addition to the standard care, the intervention group received nutritional support comprising patient education, nutrition goal setting, and the consumption of high-protein supplements. MAIN OUTCOMES MEASURES:The analysis was from a healthcare payer perspective. Key outcomes of the model included the average costs and quality-adjusted life years. Model results were tested in univariate sensitivity analyses, and decision uncertainty was characterized using a probabilistic sensitivity analysis. MAIN RESULTS:Compared with standard care, nutritional support was cost saving at AU $425 per patient and marginally more effective with an average 0.005 quality-adjusted life years gained. The probability of nutritional support being cost-effective was 87%. CONCLUSIONS:Nutritional support to prevent PrUs in high-risk hospitalized patients is cost-effective with substantial cost savings predicted. Hospitals should implement the recommendations from the current PrU practice guidelines and offer nutritional support to high-risk patients.
The Impact of Venous Leg Ulcers on Body Image and Self-esteem

OBJECTIVE:To evaluate self-esteem and body image in patients with venous leg ulcers (VLUs). DESIGN:A multicenter, prospective, descriptive, analytical, clinical study. SETTINGS:A nursing care and education center of a university hospital, a health center, and an outpatient wound care clinic in Brazil. PATIENTS:Fifty-nine consecutive adult patients with VLUs and Doppler ankle-brachial index ranging from 0.8 to 1.0 were recruited for the study. Exclusion criteria were mixed ulcers, arterial ulcers, and diabetic foot ulcers. MAIN OUTCOME MEASURES:A questionnaire assessing sociodemographic and clinical characteristics of patients, the Brazilian version of the Body Investment Scale, and the Rosenberg Self-esteem (RSE)/UNIFESP-EPM (São Paulo da Universidade Federal de São Paulo–Escola Paulista de Medicina) scale were administered to all patients. MAIN RESULTS:Most participants were women, aged between 60 and 70 years, and smokers; 33 (56%) were divorced, widowed, or single, and 26 (44%) were married. The patients had the ulcer for a mean of 5.42 years. Exudate and foul odor were present in most cases. Twenty-one ulcers (36%) measured 29 cm2 or less in surface area, and 17 (29%) ulcers measured between 30 and 49 cm2 (mean, 3.39 cm2). The mean RSE score was 22.66, indicating low self-esteem. The mean Body Investment Scale total score was 27.49, and the scores on the body image and body touch subscales were also low, indicating negative feelings about the body. CONCLUSION:Patients with VLUs had low self-esteem and negative feelings about their bodies.
The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD)*

The field of proteomics almost uniformly relies on peptide cation analysis, leading to an underrepresentation of acidic portions of proteomes, including relevant acidic posttranslational modifications. Despite the many benefits negative mode proteomics can offer, peptide anion analysis remains in its infancy due mainly to challenges with high-pH reversed-phase separations and a lack of robust fragmentation methods suitable for peptide anion characterization. Here, we report the first implementation of activated ion negative electron transfer dissociation (AI-NETD) on the chromatographic timescale, generating 7,601 unique peptide identifications from Saccharomyces cerevisiae in single-shot nLC-MS/MS analyses of tryptic peptides—a greater than 5-fold increase over previous results with NETD alone. These improvements translate to identification of 1,106 proteins, making this work the first negative mode study to identify more than 1,000 proteins in any system. We then compare the performance of AI-NETD for analysis of peptides generated by five proteases (trypsin, LysC, GluC, chymotrypsin, and AspN) for negative mode analyses, identifying as many as 5,356 peptides (1,045 proteins) with LysC and 4,213 peptides (857 proteins) with GluC in yeast—characterizing 1,359 proteins in total. Finally, we present the first deep-sequencing approach for negative mode proteomics, leveraging offline low-pH reversed-phase fractionation prior to online high-pH separations and peptide fragmentation with AI-NETD. With this platform, we identified 3,467 proteins in yeast with trypsin alone and characterized a total of 3,730 proteins using multiple proteases, or nearly 83% of the expressed yeast proteome. This work represents the most extensive negative mode proteomics study to date, establishing AI-NETD as a robust tool for large-scale peptide anion characterization and making the negative mode approach a more viable platform for future proteomic studies.
How do schools promote emotional well-being among their pupils? Findings from a national scoping survey of mental health provision in English schools.

BACKGROUND Schools play an important role in promoting child mental health, but little is known about the approaches they undertake. METHODS A scoping survey in England, involving 599 primary and 137 secondary schools. RESULTS Although two thirds of school approaches focused on all pupils, these were predominantly reactive, rather than preventive interventions. They were also largely not evidence-based, were instead based on a plan while open to adaptation. Gaps were identified in teacher training and support. CONCLUSIONS The findings have implications on the use of preventive versus reactive approaches, staff training and consultation, use of evidence-based practice in schools and joint care pathways.
Dynamic Proteome Response of Pseudomonas aeruginosa to Tobramycin Antibiotic Treatment*

Genetically susceptible bacteria become antibiotic tolerant during chronic infections, and the mechanisms responsible are poorly understood. One factor that may contribute to differential sensitivity in vitro and in vivo is differences in the time-dependent tobramycin concentration profile experienced by the bacteria. Here, we examine the proteome response induced by subinhibitory concentrations of tobramycin in Pseudomonas aeruginosa cells grown under planktonic conditions. These efforts revealed increased levels of heat shock proteins and proteases were present at higher dosage treatments (0.5 and 1 μg/ml), while less dramatic at 0.1 μg/ml dosage. In contrast, many metabolic enzymes were significantly induced by lower dosages (0.1 and 0.5 μg/ml) but not at 1 μg/ml dosage. Time course proteome analysis further revealed that the increase of heat shock proteins and proteases was most rapid from 15 min to 60 min, and the increased levels sustained till 6 h (last time point tested). Heat shock protein IbpA exhibited the greatest induction by tobramycin, up to 90-fold. Nevertheless, deletion of ibpA did not enhance sensitivity to tobramycin. It seemed possible that the absence of sensitization could be due to redundant functioning of IbpA with other proteins that protect cells from tobramycin. Indeed, inactivation of two heat shock chaperones/proteases in addition to ibpA in double mutants (ibpA/clpB, ibpA/PA0779 and ibpA/hslV) did increase tobramycin sensitivity. Collectively, these results demonstrate the time- and concentration-dependent nature of the P. aeruginosa proteome response to tobramycin and that proteome modulation and protein redundancy are protective mechanisms to help bacteria resist antibiotic treatments.
Nodular dermatofibrosis and cystic renal disease in three mixed-breed dogs and a Boxer dog.

Three mixed-breed dogs and a Boxer dog with nodular dermatofibrosis are described. The three mixed breed dogs had concurrent renal epithelial cysts (n = 2) or renal cystadenomas (n = 1); these lesions were visualized antemortem on ultrasonographic examination. One of these dogs was a 7-year-old Labrador Retriever-Gordon Setter mixed breed which survived 5 years after diagnosis, and was euthanized for unrelated causes. The Boxer dog had renal cystic adenomatous hyperplasia and renal cystadenocarcinomas which were not visualized on ultrasonographic examination but were diagnosed at necropsy.
Targeted Proteomics Identifies Paraoxonase/Arylesterase 1 (PON1) and Apolipoprotein Cs as Potential Risk Factors for Hypoalphalipoproteinemia in Diabetic Subjects Treated with Fenofibrate and Rosiglitazone*

Low levels of high-density lipoprotein cholesterol (HDL-C) and high triglyceride levels contribute to the excess rate of cardiovascular events seen in subjects with type 2 diabetes. Fenofibrate treatment partially reverses dyslipidemia in these subjects. However, a paradoxical marked reduction in HDL-C and HDL's major protein, apolipoprotein A-I, is a complication of fenofibrate in combination with rosiglitazone, an insulin-sensitizing agent. Risk factors for this condition, termed hypoalphalipoproteinemia, have yet to be identified. Using a case-control study design with subjects enrolled in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial, we tested the hypothesis that alterations in HDL's protein cargo predispose diabetic subjects to fenofibrate/rosiglitazone-induced hypoalphalipoproteinemia. HDL was isolated from blood obtained from controls (no decreases or increase in HDL-C while receiving fenofibrate/rosiglitazone therapy) and cases (developed hypoalphalipoproteinemia after fenofibrate/rosiglitazone treatment) participating in the ACCORD study before they began fenofibrate/rosiglitazone treatment. HDL proteins were quantified by targeted parallel reaction monitoring (PRM) and selected reaction monitoring (SRM) with isotope dilution. This approach demonstrated marked increases in the relative concentrations of paraoxonase/arylesterase 1 (PON1), apolipoprotein C-II (APOC2), apolipoprotein C-I, and apolipoprotein H in the HDL of subjects who developed hypoalphalipoproteinemia. The case and control subjects did not differ significantly in baseline HDL-C levels or other traditional lipid risk factors. We used orthogonal biochemical techniques to confirm increased levels of PON1 and APOC2. Our observations suggest that an imbalance in HDL proteins predisposes diabetic subjects to develop hypoalphalipoproteinemia on fenofibrate/rosiglitazone therapy.
Lung transplantation in patients with scleroderma

Purpose of reviewSystemic sclerosis (SSc) is an autoimmune disorder that involves skin and internal organs. Pulmonary diseases, comprising interstitial lung disease and pulmonary arterial hypertension, are the leading causes of morbidity and mortality in patients with SSc. Lung transplantation in patients with SSc remains controversial owing to a presumed heightened risk in the postoperative period from SSc-related gastroesophageal reflux, renal impairment, and skin fibrosis. In this article, we review the indications and patient selection criteria for lung transplantation in patients with SSc, discuss the implications and recommendations related to single versus bilateral lung transplantation, and review postlung transplantation survival data. Recent findingsEarly aggressive surgical treatment of gastroesophageal reflux disease decreases the rate of bronchiolitis and improves survival in lung transplant patients. Heart transplantations remain rare owing to frequent involvement of other organ systems in SSc patients with cardiac manifestations. The procedure of choice in patients with SSc has not been determined, but given the dearth of donor lungs, single lung transplantation has become commonplace for most SSc patients without severe pulmonary hypertension. Carefully selected patients without extrapulmonary systemic disease experience similar survival after lung transplantation compared to those with other end-stage pulmonary diseases. Patients with SSc undergoing lung transplantation have similar rates of chronic rejection as patients transplanted for nonconnective tissue disease-related interstitial lung disease. SummaryLung transplantation represents a viable therapeutic option to consider for patients with end-stage lung disease due to SSc who have limited extrapulmonary manifestations.
The Pathogenesis of the Demyelinating Form of Guillain-Barre Syndrome (GBS): Proteo-peptidomic and Immunological Profiling of Physiological Fluids*

Acute inflammatory demyelinating polyneuropathy (AIDP) - the main form of Guillain-Barre syndrome—is a rare and severe disorder of the peripheral nervous system with an unknown etiology. One of the hallmarks of the AIDP pathogenesis is a significantly elevated cerebrospinal fluid (CSF) protein level. In this paper CSF peptidome and proteome in AIDP were analyzed and compared with multiple sclerosis and control patients. A total protein concentration increase was shown to be because of even changes in all proteins rather than some specific response, supporting the hypothesis of protein leakage from blood through the blood-nerve barrier. The elevated CSF protein level in AIDP was complemented by activization of protein degradation and much higher peptidome diversity. Because of the studies of the acute motor axonal form, Guillain-Barre syndrome as a whole is thought to be associated with autoimmune response against neurospecific molecules. Thus, in AIDP, autoantibodies against cell adhesion proteins localized at Ranvier's nodes were suggested as possible targets in AIDP. Indeed, AIDP CSF peptidome analysis revealed cell adhesion proteins degradation, however no reliable dependence on the corresponding autoantibodies levels was found. Proteome analysis revealed overrepresentation of Gene Ontology groups related to responses to bacteria and virus infections, which were earlier suggested as possible AIDP triggers. Immunoglobulin blood serum analysis against most common neuronal viruses did not reveal any specific pathogen; however, AIDP patients were more immunopositive in average and often had polyinfections. Cytokine analysis of both AIDP CSF and blood did not show a systemic adaptive immune response or general inflammation, whereas innate immunity cytokines were up-regulated. To supplement the widely-accepted though still unproven autoimmunity-based AIDP mechanism we propose a hypothesis of the primary peripheral nervous system damaging initiated as an innate immunity-associated local inflammation following neurotropic viruses egress, whereas the autoantibody production might be an optional complementary secondary process.
A Strong Neutrophil Elastase Proteolytic Fingerprint Marks the Carcinoma Tumor Proteome*

Proteolytic cascades are deeply involved in critical stages of cancer progression. During the course of peptide-wise analysis of shotgun proteomic data sets representative of colon adenocarcinoma (AC) and ulcerative colitis (UC), we detected a cancer-specific proteolytic fingerprint composed of a set of numerous protein fragments cleaved C-terminally to V, I, A, T, or C residues, significantly overrepresented in AC. A peptide set linked by a common VIATC cleavage consensus was the only prominent cancer-specific proteolytic fingerprint detected. This sequence consensus indicated neutrophil elastase as a source of the fingerprint. We also found that a large fraction of affected proteins are RNA processing proteins associated with the nuclear fraction and mostly cleaved within their functionally important RNA-binding domains. Thus, we detected a new class of cancer-specific peptides that are possible markers of tumor-infiltrating neutrophil activity, which often correlates with the clinical outcome. Data are available via ProteomeXchange with identifiers: PXD005274 (Data set 1) and PXD004249 (Data set 2). Our results indicate the value of peptide-wise analysis of large global proteomic analysis data sets as opposed to protein-wise analysis, in which outlier differential peptides are usually neglected.
N-glycan MALDI Imaging Mass Spectrometry on Formalin-Fixed Paraffin-Embedded Tissue Enables the Delineation of Ovarian Cancer Tissues *

Ovarian cancer is a fatal gynaecological malignancy in adult women with a five-year overall survival rate of only 30%. Glycomic and glycoproteomic profiling studies have reported extensive protein glycosylation pattern alterations in ovarian cancer. Therefore, spatio-temporal investigation of these glycosylation changes may unearth tissue-specific changes that occur in the development and progression of ovarian cancer. A novel method for investigating tissue-specific N-linked glycans is using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) on formalin-fixed paraffin-embedded (FFPE) tissue sections that can spatially profile N-glycan compositions released from proteins in tissue-specific regions. In this study, tissue regions of interest (e.g. tumor, stroma, adipose tissue and necrotic areas) were isolated from FFPE tissue sections of advanced serous ovarian cancers (n = 3). PGC-LC-ESI-MS/MS and MALDI-MSI were used as complementary techniques to firstly generate structural information on the tissue-specific glycans in order to then obtain high resolution images of the glycan structure distribution in ovarian cancer tissue. The N-linked glycan repertoires carried by the proteins in these tissue regions were structurally characterized for the first time in FFPE ovarian cancer tissue regions, using enzymatic peptide-N-glycosidase F (PNGase F) release of N-glycans. The released glycans were analyzed by porous graphitized carbon liquid chromatography (PGC-LC) and collision induced electrospray negative mode MS fragmentation analysis. The N-glycan profiles identified by this analysis were then used to determine the location and distribution of each N-glycan on FFPE ovarian cancer sections that were treated with PNGase F using high resolution MALDI-MSI. A tissue-specific distribution of N-glycan structures identified particular regions of the ovarian cancer sections. For example, high mannose glycans were predominantly expressed in the tumor tissue region whereas complex/hybrid N-glycans were significantly abundant in the intervening stroma. Therefore, tumor and non-tumor tissue regions were clearly demarcated solely on their N-glycan structure distributions.
Effect of women’s empowerment on their utilization of health services: A case of Nepal

Over half a million women die annually due to maternity complications. Studies support that utilization of health services reduces maternal mortality. Using a nationally representative sample of 7878 previously pregnant women from Nepal we examined if gender empowerment is associated with health service use. Findings showed that three of the five indicators of empowerment – women’s age at birth of their first child, their education and knowledge about sexually transmitted diseases – significantly increased utilization of health services, especially antenatal and delivery services. Women’s opinion about wife beating and their participation in intra-household financial decisions were insignificant. Implications for social work practice are discussed.