Reducing agent-mediated precipitation of high-abundance plasma proteins

Depletion of high-abundance proteins is regarded as a critical sample preparation step for most plasma proteomic analyses and profiling strategies. This report describes a process that rapidly and reproducibly precipitates high-abundance disulfide-rich proteins, including albumin and transferrin, from serum and plasma. A low volume of concentrated reducing agent, viz. dithiothreitol (DTT) or tris(2-carboxyethyl)phosphine (TCEP), was added directly to plasma followed by a brief incubation at ambient temperature. Removal of the precipitate via centrifugation and identification of the protein content revealed an albumin-enriched pellet. Direct analysis of the supernatant by MALDI-TOF-MS afforded peptidome and small protein profiles with enhanced features and minimal ionization of full-length albumin. The reproducible and quantitative nature of the method has been demonstrated by monitoring the plasma levels of an antiangiogenic protein biologic, rKringle5 (rK5). The 10.5-kDa analyte was only reliably detected in plasma after treatment with reducing agent, ionizing linearly from 150 to 1200 fmol (on-target) with a mean CV of 7%. This method distinguishes itself from immunoaffinity resin-based approaches since it can be scaled to large milliliter quantities and it is compatible with plasma from all species tested.

Discovery, identification, and characterization of candidate pharmacodynamic markers of methionine aminopeptidase-2 inhibition

The catalytic activity of methionine aminopeptidase-2 (MetAP2) has been pharmacologically linked to cell growth, angiogenesis, and tumor progression, making this an attractive target for cancer therapy. An assay for monitoring specific protein changes in response to MetAP2 inhibition, allowing pharmacokinetic (PK)/pharmacodynamic (PD) models to be established, could dramatically improve clinical decision-making. Candidate MetAP2-specific protein substrates were discovered from undigested cell culture-derived proteomes by MALDI-/SELDI-MS profiling and a biochemical method using (35)S-Met labeled protein lysates. Substrates were identified either as intact proteins by FT-ICR-MS or applying in-gel protease digestions followed by LC-MS/MS. The combination of these approaches led to the discovery of novel MetAP2-specific substrates including thioredoxin-1 (Trx-1), SH3 binding glutamic acid rich-like protein (SH3BGRL), and eukaryotic elongation factor-2 (eEF2). These studies also confirmed glyceraldehye 3-phosphate dehydrogenase (GAPDH) and cyclophillin A (CypA) as MetAP2 substrates. Additional data in support of these proteins as MetAP2-specific substrates were provided by in vitro MetAP1/MetAP2 enzyme assays with the corresponding N-terminal derived peptides and 1D/2D Western analyses of cellular and tissue lysates. FT-ICR-MS characterization of all intact species of the 18 kDa substrate, CypA, enabled a SELDI-MS cell-based assay to be developed for correlating N-terminal processing and inhibition of proliferation. The MetAP2-specific protein substrates discovered in this study have diverse properties that should facilitate the development of reagents for testing in preclinical and clinical environments.

Exploring the learning curve in medical education: using self-assessment as a measure of learning

BACKGROUND

Learning is a complex process that follows predictable patterns. The authors explored whether students' self-assessment of competencies could be used as a measure of learning within medical school.

METHOD

Medical students (all grade levels) rated their achievement of competencies at the beginning and end of an academic year. Repeated-measures ANOVA and [eta]2 were used to determine differences.

RESULTS

Five hundred thirty-three students participated (response rate = 79.3%). Self-assessment ratings between four grade levels were significant (P < .001, [eta]2 = 0.33), with the steepest difference between MS2 and MS3; professionalism ratings remained relatively stable. The largest percent increase within an academic year occurred between MS1 and MS2, with little increase within MS3 and MS4.

CONCLUSIONS

Medical students' self-assessment ratings of competencies indicated differences between grade levels and during an academic year, following a sigmoidal curve. These results have implications for medical education and indicate the need to develop longitudinal measures to track changes in learning.

Localization of vacuolar transport receptors and cargo proteins in the Golgi apparatus of developing Arabidopsis embryos

Using immunogold electron microscopy, we have investigated the relative distribution of two types of vacuolar sorting receptors (VSR) and two different types of lumenal cargo proteins, which are potential ligands for these receptors in the secretory pathway of developing Arabidopsis embryos. Interestingly, both cargo proteins are deposited in the protein storage vacuole, which is the only vacuole present during the bent-cotyledon stage of embryo development. Cruciferin and aleurain do not share the same pattern of distribution in the Golgi apparatus. Cruciferin is mainly detected in the cis and medial cisternae, especially at the rims where storage proteins aggregate into dense vesicles (DVs). Aleurain is found throughout the Golgi stack, particularly in the trans cisternae and trans Golgi network where clathrin-coated vesicles (CCVs) are formed. Nevertheless, aleurain was detected in both DV and CCV. VSR-At1, a VSR that recognizes N-terminal vacuolar sorting determinants (VSDs) of the NPIR type, localizes mainly to the trans Golgi and is hardly detectable in DV. Receptor homology-transmembrane-RING H2 domain (RMR), a VSR that recognizes C-terminal VSDs, has a distribution that is very similar to that of cruciferin and is found in DV. Our results do not support a role for VSR-At1 in storage protein sorting, instead RMR proteins because of their distribution similar to that of cruciferin in the Golgi apparatus and their presence in DV are more likely candidates. Aleurain, which has an NPIR motif and seems to be primarily sorted via VSR-At1 into CCV, also possesses putative hydrophobic sorting determinants at its C-terminus that could allow the additional incorporation of this protein into DV.

Cross-sectional comparison of electronic and paper medical records on medication counseling in primary care clinics: a Southern Primary-Care Urban Research Network (SPUR-Net) study

INTRODUCTION

This study compared the frequency of oral counseling and written information by primary care physicians at paper medical record (PMR) clinics and electronic medical record (EMR) clinics, and assessed relationships between medication counseling and medication outcomes (knowledge, questions, reported adherence and side effects, and medication fill).

METHODS

A cross-sectional study with two convenience samples of English-speaking adult patients receiving > or =1 prescription at the primary care index visit was conducted in two PMR clinics, with 184 (48% response) patients seen by one of 22 physicians, and in two EMR clinics, with 249 (37% response) patients seen by one of 25 physicians. Data were from medical record reviews of the index visit and 2-week post-visit telephone interviews.

RESULTS

Three mutually exclusive counseling categories were evaluated. Patients received 1,095 prescriptions, 61% with oral counseling for indications, 21% with oral counseling for indications and side effects, and 12% with written information plus oral ("multi-mode") counseling. General linear mixed models found 1) less multi-mode counseling in PMR clinics (2%) than EMR clinics (20%); 2) PMR and EMR clinics were similar in oral counseling for indications and side effects; and 3) PMR clinics provided more oral counseling only for indications (69%) than EMR (53%) clinics. The impact of receiving oral or written counseling on patients' reports of having questions about their medications was inconclusive. Not receiving oral counseling for indications was associated with more questions, but not receiving written information was associated with fewer questions. Filling a prescription was lower when no oral counseling for indications and side effects was reported, but the absence of written information was associated with more prescriptions fills.

CONCLUSIONS

Physicians' use of EMR to print medication information did not seem to compromise their oral counseling for medication indications and side effects. This feature of the EMR was underutilized by physicians; however, future studies addressing patient recall and evaluating the quality and content of medication counseling are needed.

Fatty acid amide hydrolase inhibitors display broad selectivity and inhibit multiple carboxylesterases as off-targets

Fatty acid amide hydrolase (FAAH) is the primary regulator of several bioactive lipid amides including anandamide. Inhibitors of FAAH are potentially useful for the treatment of pain, anxiety, depression, and other nervous system disorders. However, FAAH inhibitors must display selectivity for this enzyme relative to the numerous other serine hydrolases present in the human proteome in order to be therapeutically acceptable. Here we employed activity-based protein profiling (ABPP) to assess the selectivity of FAAH inhibitors in multiple rat and human tissues. We discovered that some inhibitors, including carbamate compounds SA-47 and SA-72, and AM404 are exceptionally selective while others, like URB597, BMS-1, OL-135, and LY2077855 are less selective, displaying multiple off-targets. Since proteins around 60kDa constitute the major off-targets for URB597 and several other FAAH inhibitors with different chemical structures, we employed the multi-dimensional protein identification technology (MudPIT) approach to analyze their identities. We identified multiple carboxylesterase isozymes as bona fide off-targets of FAAH inhibitors. Consistently, enzymatic assay confirmed inhibition of carboxylesterase activities in rat liver by FAAH inhibitors. Since carboxylesterases hydrolyze a variety of ester-containing drugs and prodrugs, we speculate that certain FAAH inhibitors, by inhibiting carboxylesterases, might have drug-drug interactions with other medicines if developed as therapeutic agents.

A role for caleosin in degradation of oil-body storage lipid during seed germination

Caleosin is a Ca(2+)-binding oil-body surface protein. To assess its role in the degradation of oil-bodies, two independent insertion mutants lacking caleosin were studied. Both mutants demonstrated significant delay of breakdown of the 20:1 storage lipid at 48 and 60 h of germination. Additionally, although germination rates for seeds were not affected by the mutations, mutant seedlings grew more slowly than wild type when measured at 48 h of germination, a defect that was corrected with continued growth for 72 and 96 h in the light. After 48 h of germination, wild-type central vacuoles had smooth contours and demonstrated internalization of oil bodies and of membrane containing alpha- and delta-tonoplast intrinsic proteins (TIPs), markers for protein storage vacuoles. In contrast, mutant central vacuoles had distorted limiting membranes displaying domains with clumps of the two TIPs, and they contained fewer oil bodies. Thus, during germination caleosin plays a role in the degradation of storage lipid in oil bodies. Its role involves both the normal modification of storage vacuole membrane and the interaction of oil bodies with vacuoles. The results indicate that interaction of oil bodies with vacuoles is one mechanism that contributes to the degradation of storage lipid.

Association of Catsper1 or -2 with Cav3.3 Leads to Suppression of T-type Calcium Channel Activity

Sperm-specific CatSper1 and CatSper2 proteins are critical to sperm-hyperactivated motility and male fertility. Although architecturally resembling voltage-gated ion channels, neither CatSper1 nor CatSper2 alone forms functional ion channels in heterologous expression systems, which may be related to the absence of yet unidentified accessory subunits. Here we isolated CatSper1- and CatSper2-associated protein(s) from human sperm and analyzed their identities by a multidimensional protein identification technology approach. We identified the T-type voltage-gated calcium channel Ca(v)3.3 as binding to both CatSper1 and CatSper2. The specificity of their interactions was verified by co-immunoprecipitation in transfected mammalian cells. Electrophysiological studies revealed that the co-expression of CatSper1 or CatSper2 specifically inhibited the amplitude of Ca(v)3.3-evoked T-type calcium current without altering other biophysical properties of Ca(v)3.3. Immunostaining studies revealed co-localization of CatSper1 and Ca(v)3.3 on the principal piece of human sperm tail. Furthermore, fluorescence resonance energy transfer analysis revealed close proximity and physical association of these two proteins on the sperm tail. These studies demonstrate that CatSper1 and CatSper2 can associate with and modulate the function of the Ca(v)3.3 channel, which might be important in the regulation of sperm function.

Selective membrane protein internalization accompanies movement from the endoplasmic reticulum to the protein storage vacuole pathway in Arabidopsis

In plant cells, certain membrane proteins move by unknown mechanisms directly from the endoplasmic reticulum (ER) to prevacuolar or vacuole-like organelles where membrane is internalized to form a dense, lattice-like structure. Here, we identify a sequence motif, PIEPPPHH, in the cytoplasmic tail of a membrane protein that directs the protein from the ER to vacuoles where it is internalized. A type II membrane protein in Arabidopsis thaliana, (At)SRC2 (for Soybean Gene Regulated by Cold-2), binds specifically to PIEPPPHH and moves from the ER to the same vacuoles where it is internalized. Not all proteins that move in this pathway are internalized because another Arabidopsis type II membrane protein, (At)VAP (for Vesicle-Associated Protein), localizes to the same organelles but remains exposed on the limiting membrane. The identification of (At)SRC2 and its preference for interaction with a targeting motif specific for the ER-to-vacuole pathway may provide tools for future dissection of mechanisms involved in this unique trafficking system.

A unique family of proteins associated with internalized membranes in protein storage vacuoles of the Brassicaceae

The protein storage vacuole (PSV) is a specialized organelle in plant seeds that accumulates storage proteins and phytate during seed development. In many plant species, such as tomato and tobacco, the PSV contains two types of microscopically visible intra-organellar inclusions: a large crystalline lattice of membranes and proteins, the crystalloid, and one or a few large phytate crystals, the globoids. In seeds of the family Brassicaceae, the PSVs lack visible crystalloids and have many small globoids dispersed throughout. We biochemically fractionated PSVs from Brassica napus and defined a crystalloid-like fraction that contained integral membrane protein markers found in crystalloids of other plants. Protein analyses identified a previously undescribed family of proteins, the Brassicaceae PSV-embedded proteins (BPEPs), associated with 'crystalloid' and globoid fractions. The defining characteristics of the BPEPs are an N-terminal signal peptide and tandem MATH domains, which may mediate protein-protein interactions. Database analyses indicated that the BPEPs are unique to Brassicaceae. Immunofluorescence studies using anti-BPEP antibodies and antibodies to other biochemical markers to label B. napus and Arabidopsis thaliana seed sections localized the BPEPs to structures within the PSVs, whose appearance was consistent with a diffuse network of internalized membranes and globoids. These results demonstrate that Brassicaceae PSVs contain internalized membranes, and raise the possibility that BPEPs modify these internal membrane structures to yield a PSV morphology different from that of tomato or tobacco.

Purification, crystallization and preliminary crystallographic studies of the ligand-binding domain of a plant vacuolar sorting receptor

Vacuolar sorting receptor (VSR) proteins bind soluble protein ligands in a sequence-specific manner and target them to the lytic vacuole in plant cells. A VSR from Arabidopsis thaliana, AtBP80b, has been successfully purified after heterologous expression in Drosophila S2 cells. The AtBP80b protein (560 amino acids) was crystallized by the hanging-drop method with a PEG 400-based precipitant. Preliminary X-ray diffraction studies of an AtBP80b crystal showed that it belongs to the cubic space group P2(1)3 (or P4(2)32) and has unit-cell parameters a = b = c = 145.9 A. Crystals of the VSR diffract beyond 2.5 A resolution.

Observations on the teaching and learning occurring in offices of community-based family and community medicine clerkship preceptors

BACKGROUND AND OBJECTIVES

Previous reports have defined the time that community preceptors spend teaching students, but much remains to be learned about the process and content of office-based teaching. Our objective was to understand better the teaching process and content by documenting how often preceptors used the microskills described in the Five-step "Microskills" Model of Clinical Teaching and how often they discussed tasks described in the Task-oriented Processes in Care (TOPIC) teaching model when working with their students.

METHODS

Using a checklist combining these two models, two independent observers documented the teaching and learning that occurred between 12 preceptors and their students.

RESULTS

Inter-rater concordance was 96.2%. Preceptors frequently used two of the teaching microskills, "probe for supporting evidence" and "teach general rules." Preceptors and students frequently discussed many information-processing and management tasks in the TOPIC model.

CONCLUSIONS

Despite the lack of training in using either model, preceptors frequently used some teaching microskills and discussed many TOPIC model tasks. This finding supports both models as relevant teaching models but further observational study of preceptors trained in using both models is needed. For the TOPIC model, preceptor development may help preceptors to more explicitly refer to TOPIC tasks when teaching clinical content to students.

Alpha tonoplast intrinsic protein is specifically associated with vacuole membrane involved in an autophagic process

Autophagy in plant cells is induced by nutrient starvation. Initially, double membrane-bound organelles, termed autophagosomes, enclose a portion of cytoplasm, and then fuse with a vacuole or lysosome to give an autolysosome. Autolysosomes can be visualized by incubating cells in the presence of a membrane-permeable cysteine protease inhibitor. The inhibitor presumably decreases proteolytic degradation of the autolysosome contents that are composed of portions of cytoplasm enclosed by the membrane originating from the inner membrane of autophagosomes, and allows them to accumulate. The origin of membranes that give rise to autophagosomes and autolysosomes is unknown. Here we use an acidotropic fluorescent dye, LysoTracker Red, to label autolysosomes specifically. We demonstrate that autolysosome membranes are marked by the presence of alpha-tonoplast intrinsic protein (alpha-TIP) but not by gamma-TIP or delta-TIP. The identification of a TIP specifically associated with membranes derived from an autophagic process may help our understanding of how plant cells generate and maintain functionally distinct types of vacuoles.

Medical student attitudes toward the doctor-patient relationship

CONTEXT

Medical educators have emphasized the importance of teaching patient-centred care.

OBJECTIVES

To describe and quantify the attitudes of medical students towards patient-centred care and to examine: (a) the differences in these attitudes between students in early and later years of medical school; and (b) factors associated with patient-centred attitudes.

METHODS

We surveyed 673 students in the first, third, and fourth years of medical school. Our survey utilized the Patient-Practitioner Orientation Scale (PPOS), a validated instrument designed to measure individual preferences towards various aspects of the doctor-patient relationship. Total PPOS scores can range from patient-centred (egalitarian, whole person oriented) to disease- or doctor-centred (paternalistic, less attuned to psychosocial issues). Additional demographic data including gender, age, ethnicity, undergraduate coursework, family medical background and specialty choice were collected from the fourth year class.

RESULTS

A total of 510 students (76%) completed data collection. Female gender (P < 0.001) and earlier year of medical school (P = 0.03) were significantly associated with patient-centred attitudes. Among fourth year students (n = 89), characteristics associated with more patient-centred attitudes included female gender, European-American ethnicity, and primary-care career choice (P < 0.05 for each comparison).

CONCLUSION

Despite emphasis on the need for curricula that foster patient-centred attitudes among medical students, our data suggest that students in later years of medical school have attitudes that are more doctor-centred or paternalistic compared to students in earlier years. Given the emphasis placed on patient satisfaction and patient-centred care in the current medical environment, our results warrant further research and dialogue to explore the dynamics in medical education that may foster or inhibit student attitudes toward patient-centred care.

The protein storage vacuole: a unique compound organelle

Storage proteins are deposited into protein storage vacuoles (PSVs) during plant seed development and maturation and stably accumulate to high levels; subsequently, during germination the storage proteins are rapidly degraded to provide nutrients for use by the embryo. Here, we show that a PSV has within it a membrane-bound compartment containing crystals of phytic acid and proteins that are characteristic of a lytic vacuole. This compound organization, a vacuole within a vacuole whereby storage functions are separated from lytic functions, has not been described previously for organelles within the secretory pathway of eukaryotic cells. The partitioning of storage and lytic functions within the same vacuole may reflect the need to keep the functions separate during seed development and maturation and yet provide a ready source of digestive enzymes to initiate degradative processes early in germination.