Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex.

Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC complexes, and the function of most of these members remains poorly understood. SAP25, a previously identified Sin3A associated protein of 25 kDa, has been proposed to participate in regulating gene expression programs involved in the immune response but the exact mechanism of this regulation is unclear. SAP25 is not expressed in HEK293 cells, which hence serve as a natural knockout system to decipher the molecular functions uniquely carried out by this Sin3/HDAC subunit. Using molecular, proteomic, protein engineering, and interaction network approaches, we show that SAP25 interacts with distinct enzymatic and regulatory protein complexes in addition to Sin3/HDAC. While the O-GlcNAc transferase (OGT) and the TET1 /TET2/TET3 methylcytosine dioxygenases have been previously linked to Sin3/HDAC, in HEK293 cells, these interactions were only observed in the affinity purification in which an exogenously expressed SAP25 was the bait. Additional proteins uniquely recovered from the Halo-SAP25 pull-downs included the SCF E3 ubiquitin ligase complex SKP1/FBXO3/CUL1 and the ubiquitin carboxyl-terminal hydrolase 11 (USP11), which have not been previously associated with Sin3/HDAC. Finally, we use mutational analysis to demonstrate that distinct regions of SAP25 participate in its interaction with USP11, OGT/TETs, and SCF(FBXO3).) These results suggest that SAP25 may function as an adaptor protein to coordinate the assembly of different enzymatic complexes to control Sin3/HDAC-mediated gene expression.

Distinct states of nucleolar stress induced by anticancer drugs.

Ribosome biogenesis is a vital and highly energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an elevated demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing anticancer drugs on the nucleolus by screening a library of anticancer compounds for drugs that induce nucleolar stress. For a readout, a novel parameter termed 'nucleolar normality score' was developed that measures the ratio of the fibrillar center and granular component proteins in the nucleolus and nucleoplasm. Multiple classes of drugs were found to induce nucleolar stress, including DNA intercalators, inhibitors of mTOR/PI3K, heat shock proteins, proteasome, and cyclin-dependent kinases (CDKs). Each class of drugs induced morphologically and molecularly distinct states of nucleolar stress accompanied by changes in nucleolar biophysical properties. In-depth characterization focused on the nucleolar stress induced by inhibition of transcriptional CDKs, particularly CDK9, the main CDK that regulates RNA Pol II. Multiple CDK substrates were identified in the nucleolus, including RNA Pol I- recruiting protein Treacle, which was phosphorylated by CDK9 in vitro. These results revealed a concerted regulation of RNA Pol I and Pol II by transcriptional CDKs. Our findings exposed many classes of chemotherapy compounds that are capable of inducing nucleolar stress, and we recommend considering this in anticancer drug development.

Ribosomes are cell structures within a compartment called the nucleolus that are required to make proteins, which are essential for cell function. Due to their uncontrolled growth and division, cancer cells require many proteins and therefore have a particularly high demand for ribosomes. Due to this, some anti-cancer drugs deliberately target the activities of the nucleolus. However, it was not clear if anti-cancer drugs with other targets also disrupt the nucleolus, which may result in side effects. Previously, it had been difficult to study how nucleoli work, partly because in human cells they vary naturally in shape, size, and number. Potapova et al. used fluorescent microscopy to develop a new way of assessing nucleoli based on the location and ratio of certain proteins. These measurements were used to calculate a "nucleolar normality score". Potapova et al. then tested over a thousand anti-cancer drugs in healthy and cancerous human cells. Around 10% of the tested drugs changed the nucleolar normality score when compared to placebo treatment, indicating that they caused nucleolar stress. For most of these drugs, the nucleolus was not the intended target, suggesting that disrupting it was an unintended side effect. Drugs inhibiting proteins called cyclin-dependent kinases caused the most drastic changes in the size and shape of nucleoli, disrupting them completely. These kinases are known to be involved in activating enzymes required for general transcription. Potapova et al. showed that they also are involved in production of ribosomal RNA, revealing an additional role in coordinating ribosome assembly. Taken together, the findings suggest that evaluating the effect of new anti-cancer drugs on the nucleolus could help to develop future treatments with less toxic side effects. The experiments also reveal new avenues for researching how cyclin-dependent kinases control the production of RNA more generally.

Maximum power in evolution, ecology and economics.

Ludwig Boltzmann suggested that natural selection was fundamentally a struggle among organisms for available energy. Alfred Lotka argued that organisms that capture and use more energy than their competition will have a selective advantage in the evolutionary process, i.e. the Darwinian notion of evolution was based on a fundamental, generalized energy principle. He extended this general principle from the energetics of a single organism or species to the energetics of entire energy pathways through ecosystems. Howard Odum and Richard Pinkerton, building on Lotka, extended this concept to 'The maximum power principle' and applied it to many biological and physical systems including human economies. We examine this history and how these ideas relate to concepts from other disciplines including philosophy. But there has been considerable confusion in understanding and applying these concepts which we attempt to resolve while providing various examples from routine life and discussing some unresolved issues. This article is part of the theme issue 'Thermodynamics 2.0: Bridging the natural and social sciences (Part 2)'.

Serial Capture Affinity Purification and Integrated Structural Modeling of the H3K4me3 Binding and DNA Damage Related WDR76:SPIN1 Complex.

WDR76 is a multifunctional protein involved in many cellular functions. With a diverse and complicated protein interaction network, dissecting the structure and function of specific WDR76 complexes is needed. We previously demonstrated the ability of the Serial Capture Affinity Purification (SCAP) method to isolate specific complexes by introducing two proteins of interest as baits at the same time. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to the SCAP analysis of the SPIN1:SPINDOC complex, H3K4me3 was copurified with the WDR76:SPIN1 complex. In combination with crosslinking mass spectrometry, we built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Lastly, interaction network analysis of copurifying proteins revealed the potential role of the WDR76:SPIN1 complex in the DNA damage response. Teaser: In contrast to the SPINDOC/SPIN1 complex, analyses reveal that the WDR76/SPIN1 complex interacts with core histones and is involved in DNA damage.

The Pace of Life: Metabolic Energy, Biological Time, and Life History.

New biophysical theory and electronic databases raise the prospect of deriving fundamental rules of life, a conceptual framework for how the structures and functions of molecules, cells and individual organisms give rise to emergent patterns and processes of ecology, evolution and biodiversity. This framework is very general, applying across taxa of animals from 10-10 g protists to 108 g whales, and across environments from deserts and abyssal depths to rain forests and coral reefs. It has several hallmarks: 1) Energy is the ultimate limiting resource for organisms and the currency of biological fitness. 2) Most organisms are nearly equally fit, because in each generation at steady state they transfer an equal quantity of energy (22.4 kJ/g) and biomass (1 g/g) to surviving offspring. This is the equal fitness paradigm (EFP) of Brown et al. (2018). 3) The enormous diversity of life histories is due largely to variation in metabolic rates (e.g., energy uptake and expenditure via assimilation, respiration and production) and biological times (e.g., generation time). As in standard allometric and metabolic theory, most physiological and life history traits scale approximately as quarter-power functions of body mass, m (rates as ∼m-1/4 and times as ∼m1/4), and as exponential functions of temperature. 4) Time is the fourth dimension of life. Generation time is the pace of life. 5) There is, however, considerable variation not accounted for by the above scalings and existing theories. Much of this "unexplained" variation is due to natural selection on life history traits to adapt the biological times of generations to the clock times of geochronological environmental cycles. 7) Most work on biological scaling and metabolic ecology has focused on respiration rate. The emerging synthesis applies conceptual foundations of energetics and the EFP to shift the focus to production rate and generation time.

A quick method to expose the structures and relations of the middle ear and inner ear by cadaveric dissection.

INTRODUCTION: The temporal bone contains structures related to hearing and balance, and is a valuable learning resource for medical students and trainee surgeons. The middle ear and inner ear are difficult to demonstrate by cadaveric dissection as the structures are closely contained in a small space in the dense temporal bone. Consequently, the teaching and learning of the ear are largely relegated to virtual and theoretical images, and models, which has resulted in a knowledge gap in medical students and prospective surgeons. The present study aimed to elucidate a technique that exposes the structures and relations of the middle and inner ear by cadaveric dissection. MATERIALS AND METHODS: Forty-seven adult formalin-fixed cadaveric specimens were dissected by the proposed technique. The method was evaluated based on the extent of the structures exposed and time taken for dissection. RESULTS: The method exposed all the contents and relations of the middle and inner ear, including the course of the facial nerve in the petrous temporal bone, in a few minutes, without use of specialized instruments like saw, drill, endoscope, operating microscope or electric trephine. CONCLUSION: This dissection method combines maximal exposure of the structures and relations of the middle and inner ear with a short dissection time, sans use of specialized tools. It can be incorporated in the gross anatomy curriculum for medical studentsdue to the short dissection time and completeness of structures exposed. The prosected specimen can also be plastinated for use as a teaching-learning resource for medical students and surgeons.

Perturbation of BRMS1 interactome reveals pathways that impact metastasis.

Breast Cancer Metastasis Suppressor 1 (BRMS1) expression is associated with longer patient survival in multiple cancer types. Understanding BRMS1 functionality will provide insights into both mechanism of action and will enhance potential therapeutic development. In this study, we confirmed that the C-terminus of BRMS1 is critical for metastasis suppression and hypothesized that critical protein interactions in this region would explain its function. Phosphorylation status at S237 regulates BRMS1 protein interactions related to a variety of biological processes, phenotypes [cell cycle (e.g., CDKN2A), DNA repair (e.g., BRCA1)], and metastasis [(e.g., TCF2 and POLE2)]. Presence of S237 also directly decreased MDA-MB-231 breast carcinoma migration in vitro and metastases in vivo. The results add significantly to our understanding of how BRMS1 interactions with Sin3/HDAC complexes regulate metastasis and expand insights into BRMS1's molecular role, as they demonstrate BRMS1 C-terminus involvement in distinct protein-protein interactions.

Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling.

The SNF2 family ATPase Amplified in Liver Cancer 1 (ALC1) is the only chromatin remodeling enzyme with a poly(ADP-ribose) (PAR) binding macrodomain. ALC1 functions together with poly(ADP-ribose) polymerase PARP1 to remodel nucleosomes. Activation of ALC1 cryptic ATPase activity and the subsequent nucleosome remodeling requires binding of its macrodomain to PAR chains synthesized by PARP1 and NAD+ A key question is whether PARP1 has a role(s) in ALC1-dependent nucleosome remodeling beyond simply synthesizing the PAR chains needed to activate the ALC1 ATPase. Here, we identify PARP1 separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1. Investigation of these mutants has revealed multiple functions for PARP1 in ALC1-dependent nucleosome remodeling and provides insights into its multifaceted role in chromatin remodeling.

Driving integrative structural modeling with serial capture affinity purification.

Streamlined characterization of protein complexes remains a challenge for the study of protein interaction networks. Here we describe serial capture affinity purification (SCAP), in which two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multistep affinity enrichment of specific protein complexes. The multifunctional capabilities of this protein-tagging system also permit in vivo validation of interactions using acceptor photobleaching Förster resonance energy transfer and fluorescence cross-correlation spectroscopy quantitative imaging. By coupling SCAP to cross-linking mass spectrometry, an integrative structural model of the complex of interest can be generated. We demonstrate this approach using the Spindlin1 and SPINDOC protein complex, culminating in a structural model with two SPINDOC molecules docked on one SPIN1 molecule. In this model, SPINDOC interacts with the SPIN1 interface previously shown to bind a lysine and arginine methylated sequence of histone H3. Our approach combines serial affinity purification, live cell imaging, and cross-linking mass spectrometry to build integrative structural models of protein complexes.

Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network.

Despite the continued analysis of HDAC inhibitors in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The presence of two Sin3 paralogs in humans, SIN3A and SIN3B, may result in a heterogeneous population of Sin3 complexes and contributes to our poor understanding of the functional attributes of these complexes. Here, we profile the interaction networks of SIN3A and SIN3B to gain insight into complex composition and organization. In accordance with existing data, we show that Sin3 paralog identity influences complex composition. Additionally, chemical cross-linking MS identifies domains that mediate interactions between Sin3 proteins and binding partners. The characterization of rare SIN3B proteoforms provides additional evidence for the existence of conserved and divergent elements within human Sin3 proteins. Together, these findings shed light on both the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.

Integrative Modeling of a Sin3/HDAC Complex Sub-structure.

Sin3/HDAC complexes function by deacetylating histones, condensing chromatin, and modulating gene expression. Although components used to build these complexes have been well defined, we still have only a limited understanding of the structure of the Sin3/HDAC subunits assembled around the scaffolding protein SIN3A. To characterize the spatial arrangement of Sin3 subunits, we combined Halo affinity capture, chemical crosslinking, and high-resolution mass spectrometry (XL-MS) to determine intersubunit distance constraints, identifying 66 interprotein and 63 self-crosslinks for 13 Sin3 subunits. Having assessed crosslink authenticity by mapping self-crosslinks onto existing structures, we used distance restraints from interprotein crosslinks to guide assembly of a Sin3 complex substructure. We identified the relative positions of subunits SAP30L, HDAC1, SUDS3, HDAC2, and ING1 around the SIN3A scaffold. The architecture of this subassembly suggests that multiple factors have space to assemble to collectively influence the behavior of the catalytic subunit HDAC1.

Concurrently wasted and stunted 6-59 months children admitted to the outpatient therapeutic feeding programme in Karamoja, Uganda: Prevalence, characteristics, treatment outcomes and response.

This study assessed the prevalence of concurrently wasted and stunted (WaSt) children, their characteristics, treatment outcomes and response; and factors associated with time to recovery among children aged 6-59 months admitted to Outpatient Therapeutic Care (OTC) in Karamoja, Uganda. We conducted a retrospective cohort study with data from January 2016 to October 2017 for children admitted to nine OTCs in Karamoja. We defined wasted, stunted and underweight as 2.0 Z-scores below the median per WHO growth standards and < 12.5 cm for low Mid-Upper Arm Circumference (MUAC). WaSt was defined as concurrently wasted and stunted. Out of 788 eligible children included in the analysis; 48.7% (95% CI; 45.2-52.2) had WaSt. WaSt was common among males; 56.3% (95% CI; 51.3-61.3). Median age was 18 months in WaSt versus 12 months in non-WaSt children (p < 0.001). All WaSt children were underweight; and more severely wasted than non-WaSt children. During recovery, WaSt children gained weight more rapidly than non-WaSt children (2.2g/kg/day vs. 1.7g/kg/day). WaSt children had lower recovery rate (58.0% vs. 65.4%; p = 0.037). The difference in median time of recovery between WaSt and non-WaSt children (63 days vs. 56 days; p = 0.465) was not significant. Factors associated with time to recovery were children aged 24-59 months (aHR = 1.30; 95% CI;1.07-1.57;), children with MUAC 10.5-11.4 cm (aHR = 2.03; 95% CI; 1.55-2.66), MUAC ≥ 11.5 cm at admission (aHR = 3.31; 95% CI; 2.17-5.02) and living in Moroto (aHR = 3.34; 95% CI; 2.60-4.30) and Nakapiripirit (aHR = 1.95; 95% CI; 1.51-2.53) districts. The magnitude of children with WaSt in OTC shows that existing therapeutic feeding protocols could be used to detect and treat WaSt children. Further research is needed to identify and address the factors associated with sub-optimal recovery in WaSt children for effective OTC programming in Karamoja.

The 30-Year Influence of a Regional Consortium on Quality Improvement in Cardiac Surgery.

BACKGROUND: The Northern New England Cardiovascular Disease Study Group (NNECDSG) was founded in 1987 as a regional consortium to improve cardiovascular quality in Maine, New Hampshire, and Vermont. We sought to assess the longitudinal impact of the NNECDSG on quality and cost of coronary artery bypass grafting (CABG) during the past 30 years. METHODS: Patients undergoing isolated CABG at 5 medical centers from 1987-2017 were retrospectively reviewed (n = 67,942). They were divided into 4 time periods: 1987-1999 (n = 36,885), 2000-2005 (n = 14,606), 2006-2011(n = 8470), and 2012-2017 (n = 7981). The first period was the time the NNECDSG initiated a series of quality improvement initiatives including data feedback, quality improvement training, process mapping, and site visits. RESULTS: Throughout the 4 time intervals, there was a consistent decline in in-hospital mortality, from 3.4% to 1.8% despite an increase in predicted risk of mortality (P < .001), and a significant decline in in-hospital morbidity, including return to the operating room for bleeding, acute kidney injury, mediastinitis, and low output failure (P < .001). Median length of stay decreased from 7 to 5 days (P < .001), which translated into potential savings of $82,722,023. There was a decrease in use of red blood cells from 3.1 units to 2.6 units per patient in the most current time, which translated into potential savings of $1,985,456. CONCLUSIONS: By using collaborative quality improvement initiatives, the NNECDSG has succeeded in significant, sustained improvements in quality and cost for CABG during the past 30 years. These data support the utility of a regional consortium in improving quality.

Purification and enzymatic assay of class I histone deacetylase enzymes.

The reversible acetylation of histones has a profound influence on transcriptional status. Histone acetyltransferases catalyze the addition of these chemical modifications to histone lysine residues. Conversely, histone deacetylases (HDACs) catalyze the removal of these acetyl groups from histone lysine residues. As modulators of transcription, HDACs have found themselves as targets of several FDA-approved chemotherapeutic compounds which aim to inhibit enzyme activity. The ongoing efforts to develop targeted and isoform-specific HDAC inhibitors necessitates tools to study these modifications and the enzymes that maintain an equilibrium of these modifications. In this chapter, we present an optimized workflow for the isolation of recombinant protein and subsequent assay of class I HDAC activity. We demonstrate the application of this assay by assessing the activities of recombinant HDAC1, HDAC2, and SIN3B. This assay system utilizes readily available reagents and can be used to assess the activity and responsiveness of class I HDAC complexes to HDAC inhibitors.

Safety, Side Effects and Relative Efficacy of Medications for Rhythm Control of Atrial Fibrillation in Hypertrophic Cardiomyopathy.

In patients with hypertrophic cardiomyopathy (HC), atrial fibrillation (AF) is common, often poorly tolerated and difficult to treat. Limited data exists regarding safety or efficacy of drug therapy for AF rhythm control in HC patients. We performed a retrospective analysis of patients with HC followed >6 months, treated with amiodarone, sotalol, dofetilide, or disopyramide for rhythm control of non-postoperative AF. The duration followed on each medication, reasons for discontinuing, and incidences of adverse events were recorded. Confounding factors including maximum ventricular septal thickness, age, left ventricular ejection fraction, and gender were assessed. Ninety-eight patients had 130 drug treatments (defined as a continuous time on 1 drug); 23 patients were treated with >1 medication. The probability of remaining on a single antiarrhythmic drug at 1 year was 62% and at 3 was 42%. Maximum ventricular septal thickness (hazard ratio 1.05, p = 0.03) and presence of resting outflow gradient (hazard ratio 2.50, p = 0.002) were associated with discontinuation of therapy. Patients treated with amiodarone or sotalol had no serious safety events suggesting that these medications may be reasonably safe. Amiodarone was least likely to be discontinued for inefficacy (8.5%), but likely to be discontinued for side effects (19%). The probability of remaining on sotalol was 74% at 1 year and 50.0% at 3 and it was only discontinued for side effects in 2%. A small number of patients were treated with disopyramide and dofetilide. In conclusion, our data suggest that amiodarone and sotalol are likely safe, and that sotalol may be particularly attractive given its low rate of side effects and low rate of discontinuation.

Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly.

HDAC1 and HDAC2 are components of several corepressor complexes (NuRD, Sin3, CoREST and MiDAC) that regulate transcription by deacetylating histones resulting in a more compact chromatin environment. This limits access of transcriptional machinery to genes and silences transcription. While using an AP-MS approach to map HDAC1/2 protein interaction networks, we noticed that N-terminally tagged versions of HDAC1 and HDAC2 did not assemble into HDAC corepressor complexes as expected, but instead appeared to be stalled with components of the prefoldin-CCT chaperonin pathway. These N-terminally tagged HDACs were also catalytically inactive. In contrast to the N-terminally tagged HDACs, C-terminally tagged HDAC1 and HDAC2 captured complete histone deacetylase complexes and the purified proteins had deacetylation activity that could be inhibited by SAHA (Vorinostat), a Class I/II HDAC inhibitor. This tag-mediated reprogramming of the HDAC1/2 protein interaction network suggests a mechanism whereby HDAC1 is first loaded into the CCT complex by prefoldin to complete folding, and then assembled into active, functional HDAC complexes. Imaging revealed that the prefoldin subunit VBP1 colocalises with nuclear HDAC1, suggesting that delivery of HDAC1 to the CCT complex happens in the nucleus.

A Structured Workflow for Mapping Human Sin3 Histone Deacetylase Complex Interactions Using Halo-MudPIT Affinity-Purification Mass Spectrometry.

Although a variety of affinity purification mass spectrometry (AP-MS) strategies have been used to investigate complex interactions, many of these are susceptible to artifacts because of substantial overexpression of the exogenously expressed bait protein. Here we present a logical and systematic workflow that uses the multifunctional Halo tag to assess the correct localization and behavior of tagged subunits of the Sin3 histone deacetylase complex prior to further AP-MS analysis. Using this workflow, we modified our tagging/expression strategy with 21.7% of the tagged bait proteins that we constructed, allowing us to quickly develop validated reagents. Specifically, we apply the workflow to map interactions between stably expressed versions of the Sin3 subunits SUDS3, SAP30, or SAP30L and other cellular proteins. Here we show that the SAP30 and SAP30L paralogues strongly associate with the core Sin3 complex, but SAP30L has unique associations with the proteasome and the myelin sheath. Next, we demonstrate an advancement of the complex NSAF (cNSAF) approach, in which normalization to the scaffold protein SIN3A accounts for variations in the proportion of each bait capturing Sin3 complexes and allows a comparison among different baits capturing the same protein complex. This analysis reveals that although the Sin3 subunit SUDS3 appears to be used in both SIN3A and SIN3B based complexes, the SAP30 subunit is not used in SIN3B based complexes. Intriguingly, we do not detect the Sin3 subunits SAP18 and SAP25 among the 128 high-confidence interactions identified, suggesting that these subunits may not be common to all versions of the Sin3 complex in human cells. This workflow provides the framework for building validated reagents to assemble quantitative interaction networks for chromatin remodeling complexes and provides novel insights into focused protein interaction networks.

Equal fitness paradigm explained by a trade-off between generation time and energy production rate.

Most plant, animal and microbial species of widely varying body size and lifestyle are nearly equally fit as evidenced by their coexistence and persistence through millions of years. All organisms compete for a limited supply of organic chemical energy, derived mostly from photosynthesis, to invest in the two components of fitness: survival and production. All organisms are mortal because molecular and cellular damage accumulates over the lifetime; life persists only because parents produce offspring. We call this the equal fitness paradigm. The equal fitness paradigm occurs because: (1) there is a trade-off between generation time and productive power, which have equal-but-opposite scalings with body size and temperature; smaller and warmer organisms have shorter lifespans but produce biomass at higher rates than larger and colder organisms; (2) the energy content of biomass is essentially constant, ~22.4 kJ g-1 dry body weight; and (3) the fraction of biomass production incorporated into surviving offspring is also roughly constant, ~10-50%. As organisms transmit approximately the same quantity of energy per gram to offspring in the next generation, no species has an inherent lasting advantage in the struggle for existence. The equal fitness paradigm emphasizes the central importance of energy, biological scaling relations and power-time trade-offs in life history, ecology and evolution.

Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer.

Understanding the complexity of cancer biology requires extensive information about the cancer proteome over the course of the disease. The recent advances in mass spectrometry-based proteomics technologies have led to the accumulation of an incredible amount of such proteomic information. This information allows us to identify protein signatures or protein biomarkers, which can be used to improve cancer diagnosis, prognosis and treatment. For example, mass spectrometry-based proteomics has been used in breast cancer research for over two decades to elucidate protein function. Breast cancer is a heterogeneous group of diseases with distinct molecular features that are reflected in tumour characteristics and clinical outcomes. Compared with all other subtypes of breast cancer, triple-negative breast cancer is perhaps the most distinct in nature and heterogeneity. In this review, we provide an introductory overview of the application of advanced proteomic technologies to triple-negative breast cancer research.

SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down of 12 nuclear and cytoplasmic RBPs followed by quantitative mass spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1,923 human, 489 fly, and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.