Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.

The impact of different nanoparticle surface chemistry and size on uptake and toxicity in a murine macrophage cell line

This study investigated the uptake, kinetics and cellular distribution of different surface coated quantum dots (QDs) before relating this to their toxicity. J774.A1 cells were treated with organic, COOH and NH2 (PEG) surface coated QDs (40 nM). Model 20 nm and 200 nm COOH-modified coated polystyrene beads (PBs) were also examined (50 microg ml(-1)). The potential for uptake of QDs was examined by both fixed and live cell confocal microscopy as well as by flow cytometry over 2 h. Both the COOH 20 nm and 200 nm PBs were clearly and rapidly taken up by the J774.A1 cells, with uptake of 20 nm PBs being relatively quicker and more extensive. Similarly, COOH QDs were clearly taken up by the macrophages. Uptake of NH2 (PEG) QDs was not detectable by live cell imaging however, was observed following 3D reconstruction of fixed cells, as well as by flow cytometry. Cells treated with organic QDs, monitored by live cell imaging, showed only a small amount of uptake in a relatively small number of cells. This uptake was insufficient to be detected by flow cytometry. Imaging of fixed cells was not possible due to a loss in cell integrity related to cytotoxicity. A significant reduction (p<0.05) in the fluorescent intensity in a cell-free environment was found with organic QDs, NH2 (PEG) QDs, 20 nm and 200 nm PBs at pH 4.0 (indicative of an endosome) after 2 h, suggesting reduced stability. No evidence of exocytosis was found over 2 h. These findings confirm that surface coating has a significant influence on the mode of NP interaction with cells, as well as the subsequent consequences of that interaction.

Integrative analysis of RUNX1 downstream pathways and target genes

BACKGROUND: The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible for a familial platelet disorder with predisposition to acute myeloid leukemia (FPD-AML). The disruption of the largely unknown biological pathways controlled by RUNX1 is likely to be responsible for the development of leukemia. We have used multiple microarray platforms and bioinformatic techniques to help identify these biological pathways to aid in the understanding of why RUNX1 mutations lead to leukemia. RESULTS: Here we report genes regulated either directly or indirectly by RUNX1 based on the study of gene expression profiles generated from 3 different human and mouse platforms. The platforms used were global gene expression profiling of: 1) cell lines with RUNX1 mutations from FPD-AML patients, 2) over-expression of RUNX1 and CBFbeta, and 3) Runx1 knockout mouse embryos using either cDNA or Affymetrix microarrays. We observe that our datasets (lists of differentially expressed genes) significantly correlate with published microarray data from sporadic AML patients with mutations in either RUNX1 or its cofactor, CBFbeta. A number of biological processes were identified among the differentially expressed genes and functional assays suggest that heterozygous RUNX1 point mutations in patients with FPD-AML impair cell proliferation, microtubule dynamics and possibly genetic stability. In addition, analysis of the regulatory regions of the differentially expressed genes has for the first time systematically identified numerous potential novel RUNX1 target genes. CONCLUSION: This work is the first large-scale study attempting to identify the genetic networks regulated by RUNX1, a master regulator in the development of the hematopoietic system and leukemia. The biological pathways and target genes controlled by RUNX1 will have considerable importance in disease progression in both familial and sporadic leukemia as well as therapeutic implications.

Earth Science and Communities: Great Earthquakes to Wild Rice

Connections between earth science and communities are not clear to many communities. This talk explores the geologic setting, the infrastructural damage, and the impact on communities of recent large earthquakes in Taiwan, Turkey, Haiti and Japan. Decisions made about geologic hazards had a profound impact on human life and the built environment. Ridgway shares how Purdue is building connections between the scientific community and Native American communities—especially by engaging Native American students in research on tribal lands.

The Amplifier - v. 6, no. 15

In this issue...Junior Prom, Finlen Hotel, Miners baseball, Vegas Club, Ken Erickson, Texaco, The Anaconda Company, Butte Rotary Club, college drinking, Dr. Edwin G. Koch

Renal safety of annual zoledronic acid infusions in osteoporotic postmenopausal women

Intravenous bisphosphonates reduce fracture risk but have been associated in rare cases with deteriorating renal-function in cancer patients. The renal effects of zoledronic acid were assessed in osteoporotic postmenopausal women from 27 countries who received three annual infusions of zoledronic acid or a placebo in a randomized, double-blind trial. Serum creatinine, estimated creatinine clearance and urinary protein were measured before and after at least one infusion in a predefined renal safety cohort of 5035 equally divided patients. This group was compared to 7714 patients whose parameters were measured annually. Significantly more transient pre- to post-infusion increases in serum creatinine occurred in zoledronic acid than placebo-treated patients with significant elevations, relative to pre-infusion, only in the second year. All 31 zoledronic acid and 8 of 10 patients on placebo recovered their pre-infusion serum creatinine value within 12 months. No differences in mean changes in serum creatinine, estimated creatinine clearance or adverse renal events were found. We found that transient changes in renal function can occur following an annual zoledronic acid infusion but, in the long term, renal function was not different from control patients.

The lifestyle of our kids (LOOK) project: outline of methods

This methods paper outlines the overall design of a community-based multidisciplinary longitudinal study with the intent to stimulate interest and communication from scientists and practitioners studying the role of physical activity in preventive medicine. In adults, lack of regular exercise is a major risk factor in the development of chronic degenerative diseases and is a major contributor to obesity, and now we have evidence that many of our children are not sufficiently active to prevent early symptoms of chronic disease. The lifestyle of our kids (LOOK) study investigates how early physical activity contributes to health and development, utilizing a longitudinal design and a cohort of eight hundred and thirty 7-8-year-old (grade 2) school children followed to age 11-12 years (grade 6), their average family income being very close to that of Australia. We will test two hypotheses, that (a) the quantity and quality of physical activity undertaken by primary school children will influence their psychological and physical health and development; (b) compared with existing practices in primary schools, a physical education program administered by visiting specialists will enhance health and development, and lead to a more positive perception of physical activity. To test the first hypothesis we will monitor all children longitudinally over the 4 years. To test the second we will involve an intervention group of 430 children who receive two 50min physical education classes every week from visiting specialists and a control group of 400 who continue with their usual primary school physical education with their class-room teachers. At the end of grades 2, 4, and 6 we will measure several areas of health and development including blood risk factors for chronic disease, cardiovascular structure and function, physical fitness, psychological characteristics and perceptions of physical activity, bone structure and strength, motor control, body composition, nutritional intake, influence of teachers and family, and academic performance.

Ferrocene-terminated alkanethiol self-assembled monolayers: An electrochemical and in situ surface-enhanced infra-red absorption spectroscopy study

The effect of anions on the redox behavior and structure of 11-ferrocenyl-1-undecanethiol (FcC11) monolayers (SAM) on Au(1 1 1) single crystal and Au(1 1 1-25 nm) thin film electrodes was investigated in 0.1 M solutions of HPF6, HClO4, HBF4, HNO3, and H2SO4 by cyclic voltammetry (CV) and in situ surface-enhanced infrared reflection-absorption spectroscopy (SEIRAS). We demonstrate that the FcC11 redox peaks shift toward positive potentials and broaden with increasing hydrophilicity of the anions. In situ surface-enhanced IR-spectroscopy (SEIRAS) provided direct access for the incorporation of anions into the oxidized adlayer. The coadsorption of anions is accompanied by the penetration of water molecules. The latter effect is particularly pronounced in aqueous HNO3 and H2SO4 electrolytes. The adlayer permeability increases with increasing hydrophilicity of the anions. We also found that even the neutral (reduced) FcC11 SAM is permeable for water molecules. Based on the property of interfacial water to reorient upon charge inversion, we propose a spectroscopic approach for estimating the potential of zero total charge of the FcC11-modified Au(1 1 1) electrodes in aqueous electrolytes.

The role of postoperative antibiotics in facial fractures: Comparing the efficacy of a 1-day versus a prolonged regimen

BACKGROUND The goal of this study was to evaluate the influence of the duration of postoperative antibiotics (1 day vs. ≥ 5 days) on wound infections following surgical treatment of facial fractures. METHODS Three hundred thirty-nine patient case histories with a total of 498 fractures were reviewed retrospectively with regard to infections occurring within a 6-month period following surgical management. Patients were divided into two groups based on the duration of postoperative antibiotics administered. Group A consisted of 125 patients who had 1 day of postoperative antibiotics, whereas Group B consisted of 214 patients who had five or more days of postoperative antibiotics. Statistical analysis was conducted to assess for possible differences in the rate of postoperative infections. RESULTS Five patients in Group A (4%) and seven patients in Group B (3.27%) developed infections within the follow-up period. Of these 12 patients, seven had sustained multiple facial bone fractures. Eleven infections occurred in patients with mandibular fractures and one in a midfacial fracture. Statistical analysis using Fisher's exact test showed no significant difference (p = 0.77) in the incidence of infection between Groups A and B. CONCLUSION In this retrospective study, the use of prolonged postoperative antibiotics in uncomplicated mandibular and midfacial fractures had no significant benefit in reducing the incidence of infections. LEVEL OF EVIDENCE Therapeutic study, level IV.

Cattle immunized against the pathogenic L-α-glycerol-3-phosphate oxidase of Mycoplasma mycoides subs. mycoides fail to generate neutralizing antibodies and succumb to disease on challenge

The membrane-associated enzyme L-α-glycerol-3-phosphate oxidase (GlpO) of Mycoplasma mycoides subs. mycoides (Mmm), the causal agent of contagious bovine pleuropneumonia (CBPP) has been identified as a virulence factor responsible for the release of toxic by-products such as H2O2 that mediate host cell injury. Since CBPP pathogenesis is based on host inflammatory reactions, we have determined the capacity of recombinant GlpO to generate in vivo protective responses against challenge in immunized cattle. We also investigated whether sera raised against recombinant GlpO in cattle and mice inhibit production of H2O2 by Mmm. Immunization of cattle with recombinant GlpO did not protect against challenge with a virulent strain of Mmm. Further, although both murine and bovine antisera raised against recombinant GlpO detected recombinant and native forms of GlpO in immunoblot assays with similar titres, only murine antibodies could neutralize GlpO enzymatic function. The data raise the possibility that Mmm has adapted to evade potential detrimental antibody responses in its definitive host.

Interim endoscopy results during neoadjuvant therapy for gastric cancer correlate with histopathological response and prognosis

BACKGROUND Neoadjuvant chemotherapy for locally advanced gastric cancer leads to major histopathological response in less than 30 % of patients. Data on interim endoscopic response assessment do not exist. This exploratory prospective study evaluates early endoscopy after 50 % of the chemotherapy as predictor for later response and prognosis. METHODS Forty-seven consecutive patients were included (45 resected; 33 R0 resections). All patients received baseline endoscopy and CT scans, after 50 % of their chemotherapy (EGD-1, CT-1) and after completion of chemotherapy (EGD-2, CT-2). Interim endoscopic response (EGD-1) was assessed after having received 50 % (6 weeks) of the planned 12 weeks of neoadjuvant chemotherapy. Post-chemotherapy response was clinically assessed by a combination of CT scan (CT-2) and endoscopy (EGD-2). Histopathological response was determined by a standardized scoring system (Becker criteria). Endoscopic response was defined as a reduction of >75 % of the tumor mass. RESULTS Twelve patients were responders at EGD-1 and 13 at EGD-2. Nine patients (19.1 %) were clinical responders and 7 patients (15.6 %) were histopathological responders after chemotherapy. Specificity, accuracy, and negative predictive value of the interim EGD-1 for subsequent histopathological response were 31/38 (82 %), 36/47 (76 %), and 31/33 (93 %); and for recurrence or death, 28/30 (93.3 %), 38/47 (80.9 %), and 28/35 (80.0 %). Response at EGD-1 was significantly associated with histopathological response (p = 0.010), survival (p < 0.001), and recurrence-free survival (p = 0.009). CONCLUSIONS Interim endoscopy after 6 weeks predicts response and prognosis. Therefore, tailoring treatment according to interim endoscopic assessment could be feasible, but the findings of this study should be validated in a larger patient cohort.

Paleozoic-aged brine and authigenic helium preserved in an Ordovician shale aquiclude

Consideration of the geosphere for isolation of nuclear waste has generated substantial interest in the origin, age, and movement of fl uids and gases in low-permeability rock formations. Here, we present profi les of isotopes, solutes, and helium in porewaters recovered from 860 m of Cambrian to Devonian strata on the eastern fl ank of the Michigan Basin. Of particular interest is a 240-m-thick, halite-mineralized, Ordovician shale and carbonate aquiclude, which hosts Br–-enriched, post-dolomitic brine (5.8 molal Cl) originating as evaporated Silurian seawater. Authigenic helium that has been accumulating in the aquiclude for more than 260 m.y. is found to be isolated from underlying allochthonous, 3He-enriched helium that originated from the rifted base of the Michigan Basin and the Canadian Shield. The Paleozoic age and immobility of the pore fl uids in this Ordovician aquiclude considerably strengthen the safety case for deep geological repositories, but also provide new insights into the origin of deep crustal brines and opportunities for research on other components of a preserved Paleozoic porewater system.

Explanations for unsuccessful weight loss among bariatric surgery candidates.

BACKGROUND: Our objective was to analyze subjective explanations for unsuccessful weight loss among bariatric surgery candidates. METHODS: This was a retrospective analysis of 909 bariatric surgery candidates (78.2% female, average body mass index [BMI] 47.3) at a university center from 2001 to April 2007 who answered an open-ended question about why they were unable to lose weight. We generated a coding scheme for answers to the question and established inter-rater reliability of the coding process. Associations with demographic parameters and initial BMI were tested. RESULTS: The most common categories of answers were nonspecific explanations related to diet (25.3%), physical activity (21.0%), or motivation (19.7%), followed by diet-related motivation (12.7%) and medical conditions or medications affecting physical activity (12.7%). Categories related to time, financial cost, social support, physical environment, and knowledge occurred in less than 4% each. Men were more likely than women to cite a medical condition or medication affecting physical activity (19.2% vs 10.8%, P = 0.002, odds ratio [OR] = 1.96, 95% confidence interval [CI] = 1.28-2.99) but less likely to cite diet-related motivation (7.1% vs 14.2%, P = 0.008, OR = 0.46, 95% CI = 0.26-0.82). CONCLUSIONS: Our findings suggest that addressing diet, physical activity, and motivation in a comprehensive approach would meet the stated needs of obese patients. Raising patient awareness of under-recognized barriers to weight loss, such as the physical environment and lack of social support, should also be considered. Lastly, anticipating gender-specific attributions may facilitate tailoring of interventions.

Screening for obstructive sleep apnea on the internet: randomized trial.

BACKGROUND: Obstructive sleep apnea is underdiagnosed. We conducted a pilot randomized controlled trial of an online intervention to promote obstructive sleep apnea screening among members of an Internet weight-loss community. METHODS: Members of an Internet weight-loss community who have never been diagnosed with obstructive sleep apnea or discussed the condition with their healthcare provider were randomized to intervention (online risk assessment+feedback) or control. The primary outcome was discussing obstructive sleep apnea with a healthcare provider at 12 weeks. RESULTS: Of 4700 members who were sent e-mail study announcements, 168 (97% were female, age 39.5 years [standard deviation 11.7], body mass index 30.3 [standard deviation 7.8]) were randomized to intervention (n=84) or control (n=84). Of 82 intervention subjects who completed the risk assessment, 50 (61%) were low risk and 32 (39%) were high risk for obstructive sleep apnea. Intervention subjects were more likely than control subjects to discuss obstructive sleep apnea with their healthcare provider within 12 weeks (11% [9/84] vs 2% [2/84]; P=.02; relative risk=4.50; 95% confidence interval, 1.002-20.21). The number needed to treat was 12. High-risk intervention subjects were more likely than control subjects to discuss obstructive sleep apnea with their healthcare provider (19% [6/32] vs 2% [2/84]; P=.004; relative risk=7.88; 95% confidence interval, 1.68-37.02). One high-risk intervention subject started treatment for obstructive sleep apnea. CONCLUSION: An online screening intervention is feasible and likely effective in encouraging members of an Internet weight-loss community to discuss obstructive sleep apnea with their healthcare provider.