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1.
Cell Rep ; 43(5): 114220, 2024 May 11.
Artículo en Inglés | MEDLINE | ID: mdl-38735047

RESUMEN

The suprachiasmatic nucleus (SCN) encodes time of day through changes in daily firing; however, the molecular mechanisms by which the SCN times behavior are not fully understood. To identify factors that could encode day/night differences in activity, we combine patch-clamp recordings and single-cell sequencing of individual SCN neurons in mice. We identify PiT2, a phosphate transporter, as being upregulated in a population of Vip+Nms+ SCN neurons at night. Although nocturnal and typically showing a peak of activity at lights off, mice lacking PiT2 (PiT2-/-) do not reach the activity level seen in wild-type mice during the light/dark transition. PiT2 loss leads to increased SCN neuronal firing and broad changes in SCN protein phosphorylation. PiT2-/- mice display a deficit in seasonal entrainment when moving from a simulated short summer to longer winter nights. This suggests that PiT2 is responsible for timing activity and is a driver of SCN plasticity allowing seasonal entrainment.

2.
Front Med (Lausanne) ; 11: 1274688, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38515987

RESUMEN

Patients, life science industry and regulatory authorities are united in their goal to reduce the disease burden of patients by closing remaining unmet needs. Patients have, however, not always been systematically and consistently involved in the drug development process. Recognizing this gap, regulatory bodies worldwide have initiated patient-focused drug development (PFDD) initiatives to foster a more systematic involvement of patients in the drug development process and to ensure that outcomes measured in clinical trials are truly relevant to patients and represent significant improvements to their quality of life. As a source of real-world evidence (RWE), social media has been consistently shown to capture the first-hand, spontaneous and unfiltered disease and treatment experience of patients and is acknowledged as a valid method for generating patient experience data by the Food and Drug Administration (FDA). While social media listening (SML) methods are increasingly applied to many diseases and use cases, a significant piece of uncertainty remains on how evidence derived from social media can be used in the drug development process and how it can impact regulatory decision making, including legal and ethical aspects. In this policy paper, we review the perspectives of three key stakeholder groups on the role of SML in drug development, namely patients, life science companies and regulators. We also carry out a systematic review of current practices and use cases for SML and, in particular, highlight benefits and drawbacks for the use of SML as a way to identify unmet needs of patients. While we find that the stakeholders are strongly aligned regarding the potential of social media for PFDD, we identify key areas in which regulatory guidance is needed to reduce uncertainty regarding the impact of SML as a source of patient experience data that has impact on regulatory decision making.

3.
HIV Med ; 25(1): 154-160, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37772687

RESUMEN

INTRODUCTION: Since 2013, the European Testing Week (ETW) awareness campaign has become a key regional event influencing testing efforts for HIV, viral hepatitis, and sexually transmitted infections (STIs) through participation of 720 organizations. Here, we report on a survey from May to June 2022 aimed at assessing the participant-reported impact of the campaign. METHODS: All past and current participating organizations were asked to complete an online questionnaire between 12 May and 17 June 2022. Multiple choice and open-text questions included organization information, usage of ETW to engage in local testing-related activities, and the effect of a regional campaign to reach a wider audience and generate impact. RESULTS: Of the 52 respondents, 34 (65%) stated first participating in ETW 5-10 years ago. ETW was used for awareness raising by 40 respondents (83%), new testing activities by 37 (77%), advocacy initiatives by 15 (31%), and training/capacity building by 18 (38%). For awareness raising, 95% used ETW to highlight the importance of and to encourage testing; for new testing activities, 74% used ETW to reach new groups. In total, 44 (85%) reported added benefits of a Europe-wide campaign compared with national/local campaigns, particularly the increased visibility and collaboration opportunities. Impact at the local level was observed by 24 (51%), and impact at a national level was observed by 20 (43%). A total of 28 (79%) reported increases in the number of tests performed and 25 (75%) reported increases in clients accessing services. CONCLUSIONS: Regional awareness campaigns reach wider audiences, boost local and national efforts to increase testing, and sensitize key populations about the critical value of testing compared with local/national campaigns.


Asunto(s)
Infecciones por VIH , Enfermedades de Transmisión Sexual , Humanos , Infecciones por VIH/diagnóstico , Infecciones por VIH/prevención & control , Europa (Continente)/epidemiología , Encuestas y Cuestionarios
4.
Psychooncology ; 32(12): 1939-1947, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37950341

RESUMEN

OBJECTIVE: Amid the COVID-19 pandemic, healthcare providers (HCPs) of hematology patients face unique challenges due to the vulnerability of their patients. This study explores the lived experiences of these providers during and beyond the crisis. METHODS: Twenty-one Australian HCPs caring for hematology patients completed semi-structured interviews exploring their experiences and needs during the COVID-19 pandemic, adequacy of support and information provided by healthcare organizations, impact on hematology patients, and the benefits and challenges of telehealth care. Data were analyzed using reflexive thematic analysis. RESULTS: Four themes were identified: (1) Managing an initial state of flux (unsettling uncertainty and fear, unique needs of hematology patients, getting on with the job together); (2) Concerns about care provision (questioning care efficacy, burden of compassion); (3) Disconnect between HCP needs and system-level responses (burnout, isolation, and poor work-life balance, broadcast fatigue, protecting mental health), and; (4) Reflecting on the future (ongoing challenges for hematology patients, higher staff turnover and heavier workloads, innovation in the healthcare field). CONCLUSION: This study sheds light on the challenges that hematology HCPs face during and beyond the COVID-19 crisis, impacting their wellbeing. Addressing these challenges is paramount for the healthcare system at large. Provider-led peer support programs may be beneficial for addressing moral distress and building resilience. Additionally, specific consideration for the ongoing vulnerability of hematology patients could have positive impacts on providers' professional satisfaction.


Asunto(s)
COVID-19 , Humanos , Australia , COVID-19/epidemiología , Pandemias , Investigación Cualitativa , Personal de Salud
5.
J Environ Manage ; 344: 118404, 2023 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-37348304

RESUMEN

As a consequence of the rapidly growing poultry industry, chicken litter is becoming an abundant and problematic waste. Anaerobic digestion of chicken litter can mitigate environmental issues while producing valuable by-products. Recent studies have shown that leach bed reactor (LBR) systems are suitable for processing chicken litter and that anaerobic digestion can be enhanced using biochar. This study investigates the influence of biochar position within an LBR system on anaerobic digestion of chicken litter. Compared to a system without biochar, application of biochar in both the LBR (mixed in with the feedstock or as a layer below the feedstock) and coupled leachate tank (LT) increased methane yield by 6 to 8% at 51 days and accelerated VFA degradation and methane production. More significant differences in methane yield were observed at shorter solid retention times. Biochar mixed in feedstock in addition to a filter in the LT performed best in terms of both methane and hydrogen sulfide production, with a 77% reduction in hydrogen sulfide yield and hydrogen sulfide contents maintained below 500 ppm. The enhanced rates of VFA degradation and methane production when applying biochar in both reactors corresponds with observed differences in the methanogen population. Biochar application in both reactors increased the abundance of Methanobacteriales in digestate and Methanosarcinaceae in leachate compared to the control. Microbial attachment and activity on biochar also increased when mixed in feedstock. Increased diversity of the methanogen population throughout the system, as well as increased activity on biochar, may have facilitated the syntrophic relationship between acetogenic bacteria and methanogens, thus accelerating VFA degradation and methane production. These results suggest mixing biochar in feedstock, in addition to a biochar filter in the LT, to enhance anaerobic digestion of chicken litter in this system.


Asunto(s)
Pollos , Sulfuro de Hidrógeno , Animales , Anaerobiosis , Reactores Biológicos/microbiología , Metano
6.
J Proteome Res ; 22(5): 1520-1536, 2023 05 05.
Artículo en Inglés | MEDLINE | ID: mdl-37058003

RESUMEN

Protein complexes constitute the primary functional modules of cellular activity. To respond to perturbations, complexes undergo changes in their abundance, subunit composition, or state of modification. Understanding the function of biological systems requires global strategies to capture this contextual state information. Methods based on cofractionation paired with mass spectrometry have demonstrated the capability for deep biological insight, but the scope of studies using this approach has been limited by the large measurement time per biological sample and challenges with data analysis. There has been little uptake of this strategy into the broader life science community despite its rich biological information content. We present a rapid integrated experimental and computational workflow to assess the reorganization of protein complexes across multiple cellular states. The workflow combines short gradient chromatography and DIA/SWATH mass spectrometry with a data analysis toolset to quantify changes in a complex organization. We applied the workflow to study the global protein complex rearrangements of THP-1 cells undergoing monocyte to macrophage differentiation and subsequent stimulation of macrophage cells with lipopolysaccharide. We observed substantial proteome reorganization on differentiation and less pronounced changes in macrophage stimulation. We establish our integrated differential pipeline for rapid and state-specific profiling of protein complex organization.


Asunto(s)
Proteoma , Proteoma/análisis , Espectrometría de Masas/métodos , Diferenciación Celular
7.
Proteomics ; 23(7-8): e2200038, 2023 04.
Artículo en Inglés | MEDLINE | ID: mdl-36876969

RESUMEN

Data independent acquisition (DIA/SWATH) MS is a primary strategy in quantitative proteomics. diaPASEF is a recent adaptation using trapped ion mobility spectrometry (TIMS) to improve selectivity/sensitivity. Complex DIA spectra are typically analyzed with reference to spectral libraries. The best-established method for generating libraries uses offline fractionation to increase depth of coverage. More recently strategies for spectral library generation based on gas phase fractionation (GPF), where a representative sample is injected serially using narrow DIA windows that cover different mass ranges of the complete precursor space, have been introduced that performed comparably to deep offline fractionation-based libraries. We investigated whether an analogous GPF-based approach that accounts for the ion mobility (IM) dimension is useful for the analysis of diaPASEF data. We developed a rapid library generation approach using an IM-GPF acquisition scheme in the m/z versus 1/K0 space requiring seven injections of a representative sample and compared this with libraries generated by direct deconvolution-based analysis of diaPASEF data or by deep offline fractionation. We found that library generation by IM-GPF outperformed direct library generation from diaPASEF and had performance approaching that of the deep library. This establishes the IM-GPF scheme as a pragmatic approach to rapid library generation for analysis of diaPASEF data.


Asunto(s)
Biblioteca de Péptidos , Proteómica , Proteómica/métodos , Fraccionamiento Químico/métodos , Proteoma/análisis
8.
Front Psychol ; 14: 1081397, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36968693

RESUMEN

Background: There is a paucity of research examining the effects of the COVID-19 pandemic on the healthy lifestyle behaviors of hematological cancer patients. We examined changes in healthy lifestyle behaviors since the pandemic and identified factors associated with these changes among members of this high-risk population. Methods: Hematological cancer patients (n = 394) completed a self-report online survey from July to August 2020. The survey assessed pandemic-related changes in exercise, alcohol consumption, and consumption of fruit, vegetables, and wholegrains. Information relating to several demographic, clinical, and psychological factors was also collected. Factors associated with changes in healthy lifestyle behaviors were analyzed using logistic regression. Results: Just 14% of patients surveyed reported exercising more during the pandemic (39% exercised less). Only a quarter (24%) improved their diet, while nearly half (45%) reported eating less fruit, vegetables, and wholegrains. Just over a quarter (28%) consumed less alcohol (17% consumed more alcohol). Fear of contracting COVID-19 and psychological distress were significantly associated with reduced exercise. Younger age was significantly associated with both increased alcohol consumption and increased exercise. Being a woman was significantly associated with unfavorable changes in diet and being married was significantly associated with decreased alcohol consumption. Conclusion: A substantial proportion of hematological cancer patients reported unfavorable changes in healthy lifestyle behaviors during the pandemic. Results highlight the importance of supporting healthy lifestyle practices among this particularly vulnerable group to ensure health is optimized while undergoing treatment and when in remission, particularly during crisis times like the COVID-19 pandemic.

9.
Int J STD AIDS ; 33(10): 943-948, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35838040

RESUMEN

We present the outcomes of the HepHIV 2021 Lisbon & virtual conference held on 5-7 May 2021, including a Call to Action addressing policy and practice implications in the field of earlier and integrated testing for HIV, viral hepatitis, STI and TB and in light of lessons learned from the COVID-19 pandemic. Conference presentations showed that combination prevention and integrated testing and care models for multiple infectious diseases are necessary and feasible in diverse settings. Successful examples of service and system adaptations developed to mitigate impact of the pandemic were shared. Aiming to ensure greater equity in health in current and future health policies and programmes and address the adverse effects of COVID-19, we must learn from the many innovative approaches to service delivery developed in response to the pandemic, many of which have the potential to reach people whose needs were not met by existing models.


Asunto(s)
COVID-19 , Infecciones por VIH , Hepatitis Viral Humana , Enfermedades de Transmisión Sexual , Tuberculosis , Infecciones por VIH/diagnóstico , Infecciones por VIH/tratamiento farmacológico , Infecciones por VIH/epidemiología , Humanos , Pandemias , Enfermedades de Transmisión Sexual/diagnóstico , Enfermedades de Transmisión Sexual/tratamiento farmacológico , Enfermedades de Transmisión Sexual/prevención & control , Tuberculosis/diagnóstico , Tuberculosis/tratamiento farmacológico , Tuberculosis/prevención & control
10.
Artículo en Inglés | MEDLINE | ID: mdl-35162690

RESUMEN

Gay and bisexual men and other men who have sex with men (GBMSM) experience many sexual orientation-related stressors that negatively influence physical and mental health, making it imperative to understand their experiences of resilience-promoting resources such as social support. We utilized qualitative and participatory methodologies to examine sources of social support and types of social support received by GBMSM in Western Kenya through in-depth interviews with 60 GBMSM, including both peer educators and community members. GBMSM received emotional, informational, and instrumental support from six different relationship types: friends and peer groups, family of origin, sexual and romantic partners, healthcare providers, peer educators, and other people including work colleagues and police officers. A key finding from this study is the centrality of sexuality-specific support across all sources and types of support. Implications for clinics and LGBTQ organizations, policy, and future research are discussed.


Asunto(s)
Infecciones por VIH , Minorías Sexuales y de Género , Bisexualidad , Femenino , Homosexualidad Masculina/psicología , Humanos , Kenia/epidemiología , Masculino , Conducta Sexual , Apoyo Social
11.
Mol Cell ; 81(24): 5066-5081.e10, 2021 12 16.
Artículo en Inglés | MEDLINE | ID: mdl-34798055

RESUMEN

Autophagy is a conserved intracellular degradation pathway exerting various cytoprotective and homeostatic functions by using de novo double-membrane vesicle (autophagosome) formation to target a wide range of cytoplasmic material for vacuolar/lysosomal degradation. The Atg1 kinase is one of its key regulators, coordinating a complex signaling program to orchestrate autophagosome formation. Combining in vitro reconstitution and cell-based approaches, we demonstrate that Atg1 is activated by lipidated Atg8 (Atg8-PE), stimulating substrate phosphorylation along the growing autophagosomal membrane. Atg1-dependent phosphorylation of Atg13 triggers Atg1 complex dissociation, enabling rapid turnover of Atg1 complex subunits at the pre-autophagosomal structure (PAS). Moreover, Atg1 recruitment by Atg8-PE self-regulates Atg8-PE levels in the growing autophagosomal membrane by phosphorylating and thus inhibiting the Atg8-specific E2 and E3. Our work uncovers the molecular basis for positive and negative feedback imposed by Atg1 and how opposing phosphorylation and dephosphorylation events underlie the spatiotemporal regulation of autophagy.


Asunto(s)
Autofagosomas/enzimología , Proteínas Relacionadas con la Autofagia/metabolismo , Autofagia , Proteínas Quinasas/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/enzimología , Proteínas Adaptadoras Transductoras de Señales/genética , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Autofagosomas/genética , Familia de las Proteínas 8 Relacionadas con la Autofagia/genética , Familia de las Proteínas 8 Relacionadas con la Autofagia/metabolismo , Proteínas Relacionadas con la Autofagia/genética , Activación Enzimática , Regulación Enzimológica de la Expresión Génica , Regulación Fúngica de la Expresión Génica , Fosforilación , Proteínas Quinasas/genética , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Transducción de Señal , Factores de Tiempo
12.
BMC Infect Dis ; 21(Suppl 2): 874, 2021 Sep 13.
Artículo en Inglés | MEDLINE | ID: mdl-34517819

RESUMEN

BACKGROUND: Maximising access to testing by targeting more than one infection is effective in identifying new infections in settings or populations. Within the EU funded Joint Action INTEGRATE, this paper examined the feasibility and impact of expanding integrated testing for HIV, hepatitis C (HCV), chlamydia, gonorrhoea and/or syphilis in four community-based pilots through targeted interventions in Croatia, Italy and Poland and the Spring European Testing Week since community settings are key in detecting new infections and reaching key populations. METHODS: Pilots led by local INTEGRATE partners prioritised testing for other infections or key populations. The Croatian pilot expanded testing for men who have sex with men to syphilis, chlamydia and gonorrhoea. Italian partners implemented a HIV and HCV testing/information event at a migrant centre. A second Italian pilot tested migrants for HIV and HCV through outreach and a low-threshold service for people who use drugs. Polish partners tested for HIV, HCV and syphilis among people who inject drugs in unstable housing via a mobile van. Pilots monitored the number of individuals tested for each infection and reactive results. The pilot Spring European Testing Week from 18 to 25 May 2018 was an INTEGRATE-driven initiative to create more testing awareness and opportunities throughout Europe. RESULTS: The Croatian pilot found a high prevalence for each syphilis, chlamydia and gonorrhoea respectively, 2.1%, 12.4% and 6.7%. The Italian migrant centre pilot found low proportions who were previously tested for HIV (24%) or HCV (11%) and the second Italian pilot found an HCV prevalence of 6.2%, with low proportions previously tested for HIV (33%) or HCV (31%). The Polish pilot found rates of being previously tested for HIV, HCV and syphilis at 39%, 37%, and 38%, respectively. Results from the Spring European Testing Week pilot showed it was acceptable with increased integrated testing, from 50% in 2018 to 71% in 2019 in participants. CONCLUSIONS: Results show that integrated testing is feasible and effective in community settings, in reaching key populations and minimising missed testing opportunities, and the pilots made feasible because of the European collaboration and funding. For sustainability and expansion of integrated community testing across Europe, local government investment in legislation, financial and structural support are crucial.


Asunto(s)
Infecciones por VIH , Hepatitis C , Minorías Sexuales y de Género , Enfermedades de Transmisión Sexual , Sífilis , Infecciones por VIH/diagnóstico , Infecciones por VIH/epidemiología , Hepatitis C/diagnóstico , Hepatitis C/epidemiología , Homosexualidad Masculina , Humanos , Masculino , Prevalencia , Enfermedades de Transmisión Sexual/diagnóstico , Enfermedades de Transmisión Sexual/epidemiología , Enfermedades de Transmisión Sexual/prevención & control , Sífilis/diagnóstico , Sífilis/epidemiología , Sífilis/prevención & control
13.
Mol Syst Biol ; 17(8): e10240, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-34432947

RESUMEN

Advancements in mass spectrometry-based proteomics have enabled experiments encompassing hundreds of samples. While these large sample sets deliver much-needed statistical power, handling them introduces technical variability known as batch effects. Here, we present a step-by-step protocol for the assessment, normalization, and batch correction of proteomic data. We review established methodologies from related fields and describe solutions specific to proteomic challenges, such as ion intensity drift and missing values in quantitative feature matrices. Finally, we compile a set of techniques that enable control of batch effect adjustment quality. We provide an R package, "proBatch", containing functions required for each step of the protocol. We demonstrate the utility of this methodology on five proteomic datasets each encompassing hundreds of samples and consisting of multiple experimental designs. In conclusion, we provide guidelines and tools to make the extraction of true biological signal from large proteomic studies more robust and transparent, ultimately facilitating reliable and reproducible research in clinical proteomics and systems biology.


Asunto(s)
Proteómica , Espectrometría de Masas
14.
Antimicrob Agents Chemother ; 65(9): e0050421, 2021 08 17.
Artículo en Inglés | MEDLINE | ID: mdl-34228548

RESUMEN

Antimicrobial resistance (AMR) poses a threat to global health and the economy. Rifampicin-resistant Mycobacterium tuberculosis accounts for a third of the global AMR burden. Gaining the upper hand on AMR requires a deeper understanding of the physiology of resistance. AMR often results in a fitness cost in the absence of drug. Identifying the molecular mechanisms underpinning this cost could help strengthen future treatment regimens. Here, we used a collection of M. tuberculosis strains that provide an evolutionary and phylogenetic snapshot of rifampicin resistance and subjected them to genome-wide transcriptomic and proteomic profiling to identify key perturbations of normal physiology. We found that the clinically most common rifampicin resistance-conferring mutation, RpoB Ser450Leu, imparts considerable gene expression changes, many of which are mitigated by the compensatory mutation in RpoC Leu516Pro. However, our data also provide evidence for pervasive epistasis-the same resistance mutation imposed a different fitness cost and functionally distinct changes to gene expression in genetically unrelated clinical strains. Finally, we report a likely posttranscriptional modulation of gene expression that is shared in most of the tested strains carrying RpoB Ser450Leu, resulting in an increased abundance of proteins involved in central carbon metabolism. These changes contribute to a more general trend in which the disruption of the composition of the proteome correlates with the fitness cost of the RpoB Ser450Leu mutation in different strains.


Asunto(s)
ARN Polimerasas Dirigidas por ADN , Mycobacterium tuberculosis , Proteínas Bacterianas/genética , ARN Polimerasas Dirigidas por ADN/genética , Farmacorresistencia Bacteriana/genética , Pruebas de Sensibilidad Microbiana , Mutación , Mycobacterium tuberculosis/genética , Filogenia , Proteómica , Rifampin/farmacología
15.
Blood ; 138(24): 2514-2525, 2021 12 16.
Artículo en Inglés | MEDLINE | ID: mdl-34189564

RESUMEN

Many functional consequences of mutations on tumor phenotypes in chronic lymphocytic leukemia (CLL) are unknown. This may be in part due to a scarcity of information on the proteome of CLL. We profiled the proteome of 117 CLL patient samples with data-independent acquisition mass spectrometry and integrated the results with genomic, transcriptomic, ex vivo drug response, and clinical outcome data. We found trisomy 12, IGHV mutational status, mutated SF3B1, trisomy 19, del(17)(p13), del(11)(q22.3), mutated DDX3X and MED12 to influence protein expression (false discovery rate [FDR] = 5%). Trisomy 12 and IGHV status were the major determinants of protein expression variation in CLL as shown by principal-component analysis (1055 and 542 differentially expressed proteins, FDR = 5%). Gene set enrichment analyses of CLL with trisomy 12 implicated B-cell receptor (BCR)/phosphatidylinositol 3-kinase (PI3K)/AKT signaling as a tumor driver. These findings were supported by analyses of protein abundance buffering and protein complex formation, which identified limited protein abundance buffering and an upregulated protein complex involved in BCR, AKT, MAPK, and PI3K signaling in trisomy 12 CLL. A survey of proteins associated with trisomy 12/IGHV-independent drug response linked STAT2 protein expression with response to kinase inhibitors, including Bruton tyrosine kinase and mitogen-activated protein kinase kinase (MEK) inhibitors. STAT2 was upregulated in unmutated IGHV CLL and trisomy 12 CLL and required for chemokine/cytokine signaling (interferon response). This study highlights the importance of protein abundance data as a nonredundant layer of information in tumor biology and provides a protein expression reference map for CLL.


Asunto(s)
Regulación Leucémica de la Expresión Génica , Leucemia Linfocítica Crónica de Células B/genética , Mutación , Proteoma/genética , Transcriptoma , Línea Celular Tumoral , ARN Helicasas DEAD-box/genética , Humanos , Cadenas Pesadas de Inmunoglobulina/genética , Región Variable de Inmunoglobulina/genética , Fosfoproteínas/genética , Factores de Empalme de ARN/genética , Trisomía/genética
16.
Nat Commun ; 12(1): 3810, 2021 06 21.
Artículo en Inglés | MEDLINE | ID: mdl-34155216

RESUMEN

To a large extent functional diversity in cells is achieved by the expansion of molecular complexity beyond that of the coding genome. Various processes create multiple distinct but related proteins per coding gene - so-called proteoforms - that expand the functional capacity of a cell. Evaluating proteoforms from classical bottom-up proteomics datasets, where peptides instead of intact proteoforms are measured, has remained difficult. Here we present COPF, a tool for COrrelation-based functional ProteoForm assessment in bottom-up proteomics data. It leverages the concept of peptide correlation analysis to systematically assign peptides to co-varying proteoform groups. We show applications of COPF to protein complex co-fractionation data as well as to more typical protein abundance vs. sample data matrices, demonstrating the systematic detection of assembly- and tissue-specific proteoform groups, respectively, in either dataset. We envision that the presented approach lays the foundation for a systematic assessment of proteoforms and their functional implications directly from bottom-up proteomic datasets.


Asunto(s)
Isoformas de Proteínas/análisis , Proteómica/métodos , Algoritmos , Animales , Benchmarking , Humanos , Ratones , Péptidos/análisis , Péptidos/metabolismo , Isoformas de Proteínas/metabolismo , Proteómica/normas , Espectrometría de Masas en Tándem , Flujo de Trabajo
17.
Mol Syst Biol ; 17(5): e9536, 2021 05.
Artículo en Inglés | MEDLINE | ID: mdl-34032011

RESUMEN

Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data-independent acquisition proteomics (DIA/SWATH) together with a novel protein inference algorithm (xTop). We used this workflow to accurately quantify absolute protein abundances in Escherichia coli for > 2,000 proteins over > 60 growth conditions, including nutrient limitations, non-metabolic stresses, and non-planktonic states. The resulting high-quality dataset of protein mass fractions allowed us to characterize proteome responses from a coarse (groups of related proteins) to a fine (individual) protein level. Hereby, a plethora of novel biological findings could be elucidated, including the generic upregulation of low-abundant proteins under various metabolic limitations, the non-specificity of catabolic enzymes upregulated under carbon limitation, the lack of large-scale proteome reallocation under stress compared to nutrient limitations, as well as surprising strain-dependent effects important for biofilm formation. These results present valuable resources for the systems biology community and can be used for future multi-omics studies of gene regulation and metabolic control in E. coli.


Asunto(s)
Proteínas de Escherichia coli/metabolismo , Escherichia coli/crecimiento & desarrollo , Proteómica/métodos , Algoritmos , Técnicas Bacteriológicas , Escherichia coli/metabolismo , Espectrometría de Masas , Estrés Fisiológico , Biología de Sistemas , Flujo de Trabajo
18.
Methods Mol Biol ; 2259: 269-294, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33687722

RESUMEN

In living cells, most proteins are organized in stable or transient functional assemblies, protein complexes, which control a multitude of vital cellular processes such as cell cycle progression, metabolism, and signal transduction. Over several decades, specific protein complexes have been analyzed by structural biology methods, initially X-ray crystallography and more recently single particle cryoEM. In parallel, mass spectrometry (MS)-based methods including in vitro affinity-purification coupled to MS or in vivo protein proximity-dependent labeling methods have proven particularly effective to detect complexes, thus nominating new assemblies for structural analysis. Those approaches, however, are either of limited in throughput or require specifically engineered protein systems.In this chapter, we present protocols for a workflow that supports the parallel analysis of multiple complexes from the same biological sample with respect to abundance, subunit composition, and stoichiometry. It consists of the separation of native complexes by size-exclusion chromatography (SEC) and the subsequent mass spectrometric analysis of the proteins in consecutive SEC fractions. In particular, we describe (1) optimized conditions to achieve native protein complex separation by SEC, (2) the preparation of the SEC fractions for MS analysis, (3) the acquisition of the MS data at high throughput via SWATH/DIA (data-independent analysis) mass spectrometry and short chromatographic gradients, and (4) a set of bioinformatic tools for the targeted analysis of protein complexes. Altogether, the parallel measurement of a high number of complexes from a single biological sample results in unprecedented system-level insights into the remodeling of cellular protein complexes in response to perturbations of a broad range of cellular systems.


Asunto(s)
Cromatografía en Gel/métodos , Espectrometría de Masas/métodos , Proteínas/análisis , Proteómica/métodos , Cromatografía Líquida de Alta Presión/métodos , Humanos , Células Jurkat , Ultracentrifugación/métodos , Flujo de Trabajo
19.
J Virus Erad ; 7(1): 100026, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33489306

RESUMEN

INTRODUCTION: The use of pre-exposure prophylaxis (PrEP) is a safe and effective prevention option to all people at substantial risk of HIV acquisition, irrespective of gender. However, in most European countries PrEP services focus on key populations, in particular men who have sex with men (MSM). This study aims to explore PrEP availability and implementation for women across the European region. METHODS: An online survey was sent to all members of Women Against Viruses in Europe (WAVE) from 50 countries in September 2019. It consisted of 19 questions, including both multiple choice and free text answers. RESULTS: In total, responses from 34 countries were included in the study (Western Europe n â€‹= â€‹12, Central Europe â€‹= â€‹12, Eastern Europe n â€‹= â€‹6). PrEP was accessible in 30 WHO European countries. More than half of them stated that PrEP was available for all groups at-risk of HIV acquisition (n â€‹= â€‹18), while in many countries PrEP was only available to MSM and transgender persons. Two-thirds of country respondents confirmed the availability of a national guideline for PrEP (n â€‹= â€‹23), of which six countries had specific recommendations for PrEP in women. The most cited obstacles for PrEP access were lack of information about PrEP, lack of political support, and high cost for the individual. Fifteen country respondents stated that there were specific obstacles for PrEP access for women, such as guidelines prioritizing MSM, women not being seen as a target population for PrEP, and lack of knowledge about which subgroup of women would benefit most from PrEP. Seven countries had made efforts to encourage women's access to PrEP, most of which were individually based or initiated by local NGOs. CONCLUSIONS: PrEP is an important addition to HIV combination prevention. Women's access to PrEP in Europe remains limited. Women are often not included in the guidelines or targeted with education or information, resulting in a general lack of information about the use of PrEP for women.

20.
Adolescents ; 1(3): 267-282, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-35665057

RESUMEN

Gay and bisexual male youth in Kenya experience human rights violations, including pervasive stigma and discrimination, and these oppressive forces are associated with elevated rates of mental health concerns. Despite these challenges, many gay and bisexual male youth in Kenya are thriving during this critical developmental period. This study explored intrapersonal processes that gay and bisexual male youth in Kisumu, Kenya, highlight as important to developing, and demonstrating resilience in the face of adversity. We conducted qualitative in-depth interviews (IDIs) with 40 gay and bisexual male youth, ages 20-30 (mean = 26.4), and an additional 20 IDIs with gay and bisexual men, ages 22-45 (mean = 26.6), who were working as peer educators (total n = 60), all in Kisumu, Kenya. A total of nine primary themes emerged which describe various intrapersonal resilience processes enacted by gay and bisexual male youth, including sexual identity acceptance, self-confidence, self-love, religious/spiritual affirmation, adaptive coping, successful navigation, legal rights awareness, economic stability, and advocacy satisfaction. These data demonstrate the range of positive personal processes that promote mental health and wellbeing among gay and bisexual male youth in Kenya. We discuss implications of these findings for community-based interventions, and call for a research paradigm shift away from deficits and toward resilience.

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