Top Down proteomics: Facts and perspectives Catherman, Adam D.; Skinner, Owen S.; Kelleher, Neil L.
Biochemical and biophysical research communications,
03/2014, Volume:
445, Issue:
4
Journal Article
Peer reviewed
Open access
•Top Down versus Bottom Up proteomics analysis.•Separations methods for Top Down proteomics.•Developments in mass spectrometry instrumentation and fragmentation.•Native mass spectrometry.
The rise of ...the “Top Down” method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious “inference” problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100kDa to 1MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Highlights • This article comprehensively reviews intraoperative motor evoked potentials. • It then forms summary recommendations based on current evidence and expert opinion. • The International ...Society of Intraoperative Neurophysiology collaborated and endorses this position statement.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
ABSTRACT
BACKGROUND
Although surveillance for hepatocellular carcinoma (HCC) is recommended in high-risk patients, several studies have suggested it is being underutilized in clinical practice. The ...aim of our study was to quantify utilization rates for HCC surveillance among patients with cirrhosis and summarize patterns of association between utilization rates and patient socio-demographic characteristics.
DATA SOURCES
We performed a systematic literature review using the Medline database from January 1990 through March 2011 and a manual search of national meeting abstracts from 2008–2010.
METHODS
Two investigators independently extracted data on patient populations, study methods, and results using standardized forms. A pooled surveillance rate with 95% confidence intervals was calculated. Pre-specified subgroup analysis was performed to find correlates of surveillance utilization.
RESULTS
We identified nine studies that met inclusion criteria. The pooled surveillance rate was 18.4% (95%CI 17.8%–19.0%). Surveillance rates were significantly higher among patients followed in subspecialty gastroenterology clinics compared to those followed in primary care clinics (51.7% vs. 16.9%, p < 0.001). Non-Caucasians and patients of low socioeconomic status had lower surveillance rates than their counterparts.
CONCLUSIONS
Utilization rates for HCC surveillance are low, although they are significantly higher among patients followed in subspecialty clinics. Current studies fail to determine why HCC surveillance is not being performed. Future efforts should focus on identifying appropriate intervention targets to increase surveillance rates and reduce socio-demographic disparities.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Human cells are able to sense and adapt to variations in oxygen levels. Historically, much research in this field has focused on hypoxia-inducible factor (HIF) signaling and reactive oxygen species ...(ROS). Here, we perform genome-wide CRISPR growth screens at 21%, 5%, and 1% oxygen to systematically identify gene knockouts with relative fitness defects in high oxygen (213 genes) or low oxygen (109 genes), most without known connection to HIF or ROS. Knockouts of many mitochondrial pathways thought to be essential, including complex I and enzymes in Fe-S biosynthesis, grow relatively well at low oxygen and thus are buffered by hypoxia. In contrast, in certain cell types, knockout of lipid biosynthetic and peroxisomal genes causes fitness defects only in low oxygen. Our resource nominates genetic diseases whose severity may be modulated by oxygen and links hundreds of genes to oxygen homeostasis.
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•CRISPR screens at 21%, 5%, and 1% O2 highlight 322 genes, most unconnected to HIF•Low O2 buffers loss of mitochondrial and Fe-S biosynthetic pathways•Low O2 exacerbates loss of pathways in lipid and peroxisomal metabolism•Screen nominates genetic diseases that may benefit from O2-modulation
Cells in tissues experience different levels of oxygen, and investigating how individual genes contribute to fitness in response to changing oxygen tension uncovers key cellular response pathways and points to examples where modulation of oxygen levels may positively impact genetic disease.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The control arm of the phase III VIVIANE (Human PapillomaVIrus: Vaccine Immunogenicity ANd Efficacy; NCT00294047) study in women >25 years was studied to assess risk of progression from cervical HPV ...infection to detectable cervical intraepithelial neoplasia (CIN). The risk of detecting CIN associated with the same HPV type as the reference infection was analysed using Kaplan–Meier and multivariable Cox models. Infections were categorised depending upon persistence as 6‐month persistent infection (6MPI) or infection of any duration. The 4‐year interim analysis included 2,838 women, of whom 1,073 (37.8%) experienced 2,615 infections of any duration and 708 (24.9%) experienced 1,130 6MPIs. Infection with oncogenic HPV types significantly increased the risk of detecting CIN grade 2 or greater (CIN2+) versus non‐oncogenic types. For 6MPI, the highest risk was associated with HPV‐33 (hazard ratio HR: 31.9 8.3–122.2, p < 0.0001). The next highest risk was with HPV‐16 (21.1 6.3–70.0, p < 0.0001). Similar findings were seen for infections of any duration. Significant risk was also observed for HPV‐18, HPV‐31, and HPV‐45. Concomitant HPV infection or CIN grade 1 or greater associated with a different oncogenic HPV type increased risk. Most women (79.3%) with an HPV infection at baseline cleared detectable infections of any duration, and 69.9% cleared a 6MPI. The risk of progression of HPV infection to CIN2+ in women >25 years in this study was similar to that in women 15–25 years in PATRICIA.
What's New?
Which HPV infections lead to cancer in women over 25 years? Most cervical cancer follows persistent oncogenic HPV infection, but most HPV infections clear naturally. Thus, to best predict patient outcomes, it's imperative to understand how HPV infections progress to CINs. This study confirmed that in women over 25 years, persistent infection with HPV‐33 or HPV‐16 meant the greatest chance of developing a CIN—the same as was found in women 15–25 years, in an earlier analysis.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
•The Nanopatch is a high-density array of micro-projections for vaccine delivery to the skin.•The first clinical study with the Nanopatch has been performed.•There were no unexpected adverse ...events.•All applications resulted in erythema; the skin response was visible for several days or weeks.•Applications were mostly pain-free; 15/18 subjects preferred the Nanopatch to needle and syringe.
Most vaccinations are performed by intramuscular injection with a needle and syringe. However, this method is not ideal due to limitations, such as the risk of needle-stick injury, the requirement for trained personnel to give injections and the need to reconstitute lyophilized vaccines. Therefore, we tested an alternative delivery technology that overcomes the problems with needle and syringe. The Nanopatch™ is an array of 10,000 silicon micro-projections per cm2 that can be dry-coated with vaccine for skin delivery. The high number and density of micro-projections means that high velocity application is required to achieve consistent skin penetration. Before clinically testing a vaccine Nanopatch, this study tests the safety, tolerability and acceptability/utility of uncoated and excipient-coated Nanopatches in healthy adults.
Nanopatches were applied to skin of the upper arm and volar forearm and left in contact with the skin for two minutes before removal. The application sites were assessed for local skin response over 28 days. Acceptability interviews were also performed.
No unexpected adverse events directly related to the Nanopatch application were reported. All applications of the Nanopatch resulted in an expected erythema response which faded between days 3 and 7. In some subjects, some skin discolouration was visible for several days or up to 3 weeks after application. The majority (83%) of subjects reported a preference for the Nanopatch compared to the needle and syringe and found the application process to be simple and acceptable. On a pain scale from 0 to 10, 78% of applications were scored “0” (no pain) with the average scores for less than 1.
The results from this study demonstrate the feasibility of the Nanopatch to improve vaccination by showing that application of the product without vaccine to human skin is safe, tolerable and preferred to needle and syringe administration.
Clinical trial registry ID: ACTRN1261500083549.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
•This article reviews and forms recommendations for intraoperative SEPs.•It endorses SEP optimization to enhance surgical feedback speed and accuracy.•It supports an adaptive warning criterion to ...adjust for baseline drift and variability.
Intraoperative somatosensory evoked potentials (SEPs) provide dorsal somatosensory system functional and localizing information, and complement motor evoked potentials. Correct application and interpretation require in-depth knowledge of relevant anatomy, electrophysiology, and techniques. It is advisable to facilitate cortical SEPs with total intravenous propofol–opioid or similarly favorable anesthesia. Moreover, SEP optimization is recommended to enhance surgical feedback speed and accuracy by maximizing signal-to-noise ratio (SNR); it consists of selecting highest-SNR peripheral and cortical derivations while omitting low-SNR channels. Confounding factors causing non-surgical SEP reduction should be excluded before issuing a warning. It is advisable to facilitate their identification with peripheral SEP controls and cortical SEP systemic controls whenever possible. Warning criteria should adjust for baseline drift and reproducibility. The recommended adaptive warning criterion is visually obvious amplitude reduction from recent pre-change values and clearly exceeding trial-to-trial variability, particularly when abrupt and focal. Acquisition and interpretation should be done by qualified technical and professional level personnel. Indications for SEP monitoring include intracranial, posterior fossa, and spinal neurosurgery, as well as orthopedic spine, cerebrovascular, and descending aortic surgery. Indications for SEP mapping include sensorimotor cortex and dorsal column midline identification. Future advances could modify current recommendations.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
•Recovery of motor evoked potential (MEP) deterioration depended on the intraoperative event associated with the alert.•A structural causal model predicted outcomes for MEP alerts after adjustments ...for confounding.•Recovery of MEP deterioration is a strong and independent predictor of no new motor deficits.
To improve estimates of motor evoked potential (MEP) performance during spine deformity surgeries by accounting for potential confounders.
A meta-analysis of MEPs for spine deformity surgeries determined the probability of a MEP deterioration which recovered by the end of surgery, P(RSC), and the conditional probability of no new post-operative deficit given an RSC, P(NND|RSC), stratified by category of intraoperative adverse event associated with the MEP deterioration. A structural causal model (SCM) and propensity score matching accounted for intraoperative adverse events and patient diagnosis as potential confounders.
MEPs changes (either reversible, RSC or irreversible, IRREV) were reported for 295 of 5055 cases (6%) in 21 studies. The probability of no new motor deficit, P(NND), plotted against the probability of a RSC, P(RSC), for studies in the meta-analysis was highly significant (r = 0.71, p < 0.001). P(RSC) was 0.76 for an alert associated with correction, less for osteotomies (0.48, p = 0.0008), and tended to be higher for hypotension (0.92, p = 0.06). P(NND|RSC) was 0.94 for correction, less for positioning (0.82), and osteotomies (0.86), and greater for hypotension (1.0). In the SCM, a RSC after an alert was a highly significant and independent predictor of no new motor deficits (odds 25.2, p < 0.001).
There are significant differences in P(RSC) for hypotension and osteotomies, and in P(NND) for osteotomies and instrumentation, compared to correction. P(RSC) is a significant and independent predictor of outcomes.
When MEPs are used for spine deformity surgeries, accounting for adverse events associated with an alert and patient diagnosis as potential confounders is expected to improve RSC prediction of post-operative outcomes and estimates of RSC efficacy in improving outcomes.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
There is evidence from human twin and family studies as well as mouse and rat selection experiments that there are considerable interindividual differences in the response of cardiorespiratory ...fitness (CRF) and other cardiometabolic traits to a given exercise programme dose. We developed this consensus statement on exercise response variability following a symposium dedicated to this topic. There is strong evidence from both animal and human studies that exercise training doses lead to variable responses. A genetic component contributes to exercise training response variability.In this consensus statement, we (1) briefly review the literature on exercise response variability and the various sources of variations in CRF response to an exercise programme, (2) introduce the key research designs and corresponding statistical models with an emphasis on randomised controlled designs with or without multiple pretests and post-tests, crossover designs and repeated measures designs, (3) discuss advantages and disadvantages of multiple methods of categorising exercise response levels-a topic that is of particular interest for personalised exercise medicine and (4) outline approaches that may identify determinants and modifiers of CRF exercise response. We also summarise gaps in knowledge and recommend future research to better understand exercise response variability.
Most observers see rising health care costs as an inexorable force. Dr. Elliott Fisher, Dr. Julie Bynum, and Jonathan Skinner write that by learning from regions that have attained sustainable growth ...rates and building on successful models of delivery-system and payment-system reform, we might manage to “bend the cost curve.”
The expansion of health insurance coverage in the United States is likely to be on the front burner of health care reform efforts in the new presidential administration. But boiling on the back burner is perhaps the most serious threat to Americans' access to care: rapid growth in health care costs.
Pessimism abounds. Most observers see rising costs as an inexorable force, blame advancing technology, and conclude that only by rationing beneficial care or making draconian price cuts can we slow the growth of health care costs.
But a careful look at variations in spending growth and spending patterns among . . .
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