Acetylated microtubules are required for fusion of autophagosomes with lysosomes

Background  

Autophagy is a dynamic process during which isolation membranes package substrates to form autophagosomes that are fused with lysosomes to form autolysosomes for degradation. Although it is agreed that the LC3II-associated mature autophagosomes move along microtubular tracks, it is still in dispute if the conversion of LC3I to LC3II before autophagosomes are fully mature and subsequent fusion of mature autophagosomes with lysosomes require microtubules.     

Processing methods for differential analysis of LC/MS profile data

Background  

Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. One of the major challenges in this domain remains development of better solutions for processing of LC/MS data.     

Highly sensitive feature detection for high resolution LC/MS

Background  

Liquid chromatography coupled to mass spectrometry (LC/MS) is an important analytical technology for e.g. metabolomics experiments. Determining the boundaries, centres and intensities of the two-dimensional signals in the LC/MS raw data is called feature detection. For the subsequent analysis of complex samples such as plant extracts, which may contain hundreds of compounds, corresponding to thousands of features – a reliable feature detection is mandatory.     

MiR-204 regulates cardiomyocyte autophagy induced by ischemia-reperfusion through LC3-II

Background  

Autophagy plays a significant role in myocardial ischemia-reperfusion (IR) injury. So it is important to inhibit autophagy to protect cardiomyocytes besides anti-apoptosis. MiRNA has been demonstrated to protect cardiomyocytes against apoptosis during IR, while whether it has anti-autophagy effect has not been known. The aim of this study was to investigate whether miR-204 regulated autophagy by regulating LC3-II protein, which is the marker of autophagosome during myocardial IR injury.     

Proteome of the phytopathogen <Emphasis Type="Italic">Xanthomonas citri</Emphasis> subsp. <Emphasis Type="Italic">citri</Emphasis>: a global expression profile

Background  

Citrus canker is a disease caused by Xantomonas citri subsp.citri (Xac), and has emerged as one of the major threats to the worldwide citrus crop because it affects all commercial citrus varieties, decreases the production and quality of the fruits and can spread rapidly in citrus growing areas. In this work, the first proteome of Xac was analyzed using two methodologies, two-dimensional liquid chromatography (2D LC) and tandem mass spectrometry (MS/MS).     

Comparison of lung cancer cell lines representing four histopathological subtypes with gene expression profiling using quantitative real-time PCR

Background  

Lung cancers are the most common type of human malignancy and are intractable. Lung cancers are generally classified into four histopathological subtypes: adenocarcinoma (AD), squamous cell carcinoma (SQ), large cell carcinoma (LC), and small cell carcinoma (SC). Molecular biological characterization of these subtypes has been performed mainly using DNA microarrays. In this study, we compared the gene expression profiles of these four subtypes using twelve human lung cancer cell lines and the more reliable quantitative real-time PCR (qPCR).     

Metabolic effects of low cortisol during exercise in humans

This studyexamined the physiological effect of reduced plasma cortisol (C) duringprolonged exercise in humans. The effects of normal C (NC) werecompared with metyrapone-induced low C (LC) on plasma substrateavailability and the respiratory exchange ratio during 2 h of exerciseat ~60% peak O₂ consumption innine subjects. The C responses were compared with preexercise (Pre) levels and with a rest day (Con). At rest, C was attenuated by ~70%for LC compared with NC. At rest, plasma glucose, lactate, glycerol,-hydroxybutyrate, alanine, branched-chain amino acids, insulin,glucagon, growth hormone, epinephrine, and norepinephrine were similarunder LC and NC (P > 0.05). Duringexercise under NC, plasma C increased compared with Pre, whereas itremained unchanged during LC. During NC, plasma C was elevated at 90 min (compared with Con) and at 120 min (compared with Con and Pre). During exercise, plasma glucose decreased to the same extent and lactate was similar under both conditions, whereas plasma glycerol, -hydroxybutyrate, alanine, and branched-chain amino acids were higher (P < 0.01) under NC. Plasmainsulin declined (P = 0.01) to agreater extent under LC, whereas growth hormone, epinephrine, andnorepinephrine tended to be higher (0.05  P  0.10). Plasma glucagon increasedunder both conditions (P < 0.01).The respiratory exchange ratio did not differ between conditions. Weconclude that, during exercise, 1) Caccelerates lipolysis, ketogenesis, and proteolysis;2) under LC, glucoregulatory hormoneadjustments maintain glucose homeostasis; and3) LC does not alter whole body substrate utilization or the ability to complete 2 h of moderate exercise.

     

MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments

Background  

Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides on time-of-flight (TOF) instruments: LC peak boundary detection, thermal noise suppression, interference removal and mass drift correction. We propose to use the Maximum Ratio Combining (MRC) method to extract MS signal templates for interference detection/removal and LC peak boundary detection. In our method, MRCQuant, MS templates are extracted directly from experimental values, and the mass drift in each LC-MS run is automatically captured and compensated. We compared the quantification accuracy of MRCQuant to that of another representative LC-MS quantification algorithm (msInspect) using datasets downloaded from a public data repository.     

A Meta-Analysis of Reference Values of Leptin Concentration in Healthy Postmenopausal Women

Objective

There are numerous reports about the leptin concentration (LC) in postmenopausal women (PW). Changes in LC can elicit different clinical outcomes. We systematically analyzed the LC in PW.

Methods

A search was conducted in original English-language studies published from 1994 to October 2012 in the following databases: Medline (78), Cochrane Center (123) Embase (505), Biological abstracts (108), Cochrane (53) and Science Finder Scholar (0). A meta-analysis was undertaken on the correction coefficient (r) between the serum LC and body mass index (BMI) for healthy PW across studies containing a dataset and sample size. Pre-analytical and analytical variations were examined. Pre-analytical variables included fasting status (FS) and sampling timing. Analytical variation comprised assay methodology, LC in those undertaking hormone replacement therapy (HRT) and those not having HRT as well as LC change according to age.

Results

Twenty-seven studies met the inclusion criteria. Eighteen studies detected LC in the morning in a FS, 15 studies denoted the r between leptin and the BMI. A combined r was counted for the 15 studies (r = 0.51 [95% confidence interval (CI), 0.46–0.54], P = 0.025), and if sampling collection was in the FSat morning, a combined r was form 10 studies (r = 0.54 [95% CI, 0.45–0.54], P = 0.299) and heterogeneity was diminished. LC did not change between HRT users and non-users in 7 studies. Five studies analyzed changes in LC according to age.

Conclusion

Based on all studies that investigated both LC and BMI, LC was positively correlated with the BMI. No studies established reference ranges according to the Clinical and Laboratory Standards Institute (CLSI) in healthy PW, and there was a wide variation in LC values. These differences suggest that caution should be used in the interpretation and comparison between studies.     

A simple method to determine IgG light chain to heavy chain polypeptide ratios expressed by CHO cells

Objectives

To establish a high-throughput method for determination of antibodies intra- and extracellular light chain (LC) to heavy chain (HC) polypeptide ratio as screening parameter during cell line development.

Results

Chinese Hamster Ovary (CHO) TurboCell pools containing different designed vectors supposed to result in different LC:HC polypeptide ratios were generated by targeted integration. Cell culture supernatants and cell lysates of a fed batch experiment were purified by combined Protein A and anti-kappa affinity batch purification in 96-well format. Capture of all antibodies and their fragments allowed the determination of the intra- and extracellular LC:HC peptide ratios by reduced SDS capillary electrophoresis. Results demonstrate that the method is suitable to show the significant impact of the vector design on the intra- and extracellular LC:HC polypeptide ratios.

Conclusion

Determination of LC:HC polypeptide ratios can give important information in vector design optimization leading to CHO cell lines with optimized antibody assembly and preferred product quality.

     

Reproducibility of In-Vivo OCT Measured Three-Dimensional Human Lamina Cribrosa Microarchitecture

Purpose

To determine the reproducibility of automated segmentation of the three-dimensional (3D) lamina cribrosa (LC) microarchitecture scanned in-vivo using optical coherence tomography (OCT).

Methods

Thirty-nine eyes (8 healthy, 19 glaucoma suspects and 12 glaucoma) from 49 subjects were scanned twice using swept-source (SS−) OCT in a 3.5×3.5×3.64 mm (400×400×896 pixels) volume centered on the optic nerve head, with the focus readjusted after each scan. The LC was automatically segmented and analyzed for microarchitectural parameters, including pore diameter, pore diameter standard deviation (SD), pore aspect ratio, pore area, beam thickness, beam thickness SD, and beam thickness to pore diameter ratio. Reproducibility of the parameters was assessed by computing the imprecision of the parameters between the scans.

Results

The automated segmentation demonstrated excellent reproducibility. All LC microarchitecture parameters had an imprecision of less or equal to 4.2%. There was little variability in imprecision with respect to diagnostic category, although the method tends to show higher imprecision amongst healthy subjects.

Conclusion

The proposed automated segmentation of the LC demonstrated high reproducibility for 3D LC parameters. This segmentation analysis tool will be useful for in-vivo studies of the LC.     

An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters

Background  

Many studies have provided algorithms or methods to assess a statistical significance in quantitative proteomics when multiple replicates for a protein sample and a LC/MS analysis are available. But, confidence is still lacking in using datasets for a biological interpretation without protein sample replicates. Although a fold-change is a conventional threshold that can be used when there are no sample replicates, it does not provide an assessment of statistical significance such as a false discovery rate (FDR) which is an important indicator of the reliability to identify differentially expressed proteins. In this work, we investigate whether differentially expressed proteins can be detected with a statistical significance from a pair of unlabeled protein samples without replicates and with only duplicate LC/MS injections per sample. A FDR is used to gauge the statistical significance of the differentially expressed proteins.     

Proteomic analysis of the fish pathogen <Emphasis Type="Italic">Flavobacterium columnare</Emphasis>

Background  

Flavobacterium columnare causes columnaris disease in cultured and wild fish populations worldwide. Columnaris is the second most prevalent bacterial disease of commercial channel catfish industry in the United States. Despite its economic importance, little is known about the expressed proteins and virulence mechanisms of F. columnare. Here, we report the first high throughput proteomic analysis of F. columnare using 2-D LC ESI MS/MS and 2-DE MALDI TOF/TOF MS.     

Correlation between Lamina Cribrosa Tilt Angles,Myopia and Glaucoma Using OCT with a Wide Bandwidth Femtosecond Mode-Locked Laser

Purpose

To measure horizontal and vertical lamina cribrosa (LC) tilt angles and investigate associated factors using prototype optical coherence tomography (OCT) with a broad wavelength laser light source.

Design

Cross sectional study.

Methods

Twenty-eight no glaucoma eyes (from 15 subjects) and 25 glaucoma eyes (from 14 patients) were enrolled. A total of 300 optic nerve head B-scans were obtained in 10 µm steps and the inner edge of Bruch''s membrane opening (BMO) was identified as the reference plane. The vertical and horizontal angles between BMO line and approximate the best-fitting line for the surface of the LC were measured and potential associated factors were estimated with univariate and multivariate logistic regression analyses.

Results

The median (interquartile range) horizontal and vertical tilt angles were 7.10 (2.43–11.45) degrees and 4.15 (2.60–6.85) degrees in eyes without glaucoma and 8.50 (4.40–14.10) degrees and 9.30 (6.90–14.15) degrees in glaucoma eyes, respectively. The refractive errors had a statistically significant association with horizontal LC tilt angles (coefficients, −1.53 per diopter) and glaucoma had a significant correlation with vertical tilt angles (coefficients, 6.56) using multiple logistic regression analysis (p<0.001).

Conclusions

OCT allowed evaluation of the internal tilting of the LC compared with the BMO. The horizontal internal LC tilt angle was correlated with refractive errors, corresponding to myopic physiological changes, and vertical internal LC tilt was correlated with glaucoma, corresponding to glaucomatous pathological changes. These parameters have important implications for investigation of the correlation between myopia, glaucoma and LC morphological features.     

Association Analysis between SNPs in IL-28B Gene and the Progress of Hepatitis B Infection in Han Chinese

Objective

As a candidate gene association study, we investigated the genetic association of SNPs in IL-28B genes with different outcomes of HBV infection, including LC and HCC occurrence.

Methods

Chinese Han subjects were categorized into two groups: 406 LC caused by CHB and 406 HCC caused by CHB. Genomic DNA was isolated from whole blood samples, SNPs were detected using high resolution melting curve (HRM) method. PCR amplification was carried out under the same conditions in a 96-well plate in Real-Time PCR System. Then 341 LC and 356 HCC patients caused by HBV infection were analyzed as a verification by independent sample. 393 CHB patients and 244 health subjects were included as control.

Results

CHB patients who progress to LC or HCC showed a significant different frequency in rs12979860 (p = 0.046). Patients with HCC carried more frequently the T alleles in rs12979860 comparison to LC. Same results were found in the independent sample.

Conclusion

IL-28B rs12979860 C/T polymorphism T allele appears to be more prevalent in patients with HCC than in LC. Carriage of this allele seems to enhance the risk for developing HCC. Gene polymorphism of IL-28B may confer symptomatic specificity in progress and extent of hepatitis B infection.     

3D Evaluation of the Lamina Cribrosa with Swept-Source Optical Coherence Tomography in Normal Tension Glaucoma

Purpose

Although the lamina cribrosa (LC) is the primary site of axonal damage in glaucoma, adequate methods to image and measure it are currently lacking. Here, we describe a noninvasive, in vivo method of evaluating the LC, based on swept-source optical coherence tomography (SS-OCT), and determine this method’s ability to quantify LC thickness.

Methods

This study comprised 54 eyes, including normal (n = 18), preperimetric glaucoma (PPG; n = 18), and normal tension glaucoma (NTG; n = 18) eyes. We used SS-OCT to obtain 3 x 3 mm cube scans of an area centered on the optic disc, and then synchronized reconstructed B- and en-face images from this data. We identified the LC in these B-scan images by marking the visible borders of the LC pores. We marked points on the anterior and posterior borders of the LC in 12 B-scan images in order to create a skeleton model of the LC. Finally, we used B-spline interpolation to form a 3D model of the LC, including only reliably measured scan areas. We calculated the average LC thickness (avgLCT) in this model and used Spearman''s rank correlation coefficient to compare it with circumpapillary retinal nerve fiber layer thickness (cpRNFLT).

Results

We found that the correlation coefficient of avgLCT and cpRNFLT was 0.64 (p < 0.01). The coefficient of variation for avgLCT was 5.1%. AvgLCT differed significantly in the groups (normal: 282.6 ± 20.6 μm, PPG: 261.4 ± 15.8 μm, NTG: 232.6 ± 33.3 μm). The normal, PPG and NTG groups did not significantly differ in age, sex, refractive error or intraocular pressure (IOP), although the normal and NTG groups differed significantly in cpRNFLT and Humphrey field analyzer measurements of mean deviation.

Conclusion

Thus, our results indicate that the parameters of our newly developed method of measuring LC thickness with SS-OCT may provide useful and important data for glaucoma diagnosis and research.     

Expression of Autophagy-Related Proteins According to Androgen Receptor and HER-2 Status in Estrogen Receptor-Negative Breast Cancer

Purpose

The purpose of this study was to investigate the expression of autophagy-related proteins in relation to androgen receptor (AR) status in estrogen receptor (ER)-negative breast cancers.

Methods

We extracted 334 ER-negative breast cancer samples to construct tissue microarrays (TMAs), which were immunohistochemically stained for autophagy-related proteins (beclin-1, LC3A, LC3B, p62) and for AR and HER-2.

Results

There were 127 AR-positive cases and 207 AR-negative cases, and 140 HER-2-positive cases and 194 HER-2 negative cases. The AR-negative group was associated with tumoral LC3A expression (P<0.001), while the AR-positive group was associated with tumoral BNIP3 expression (P<0.001). Tumoral LC3A was most highly expressed in the AR-negative and HER-2 negative group, while stromal LC3A showed the highest expression in the AR-negative and HER-2-positive group. Tumoral BNIP3 and stromal BNIP3 were highest in the AR-positive and HER-2-negative group. In the AR-positive and HER-2-negative group, stromal p62 positivity was an independent factor that was statistically significant in its association with shorter disease-free survival (DFS) (Hazard ratio: 10.21, 95% CI: 1.130–92.31, P = 0.039). Shorter DFS was associated with tumoral LC3A positivity (Hazard ratio: 10.28, 95% CI: 2.068–51.19, P = 0.004) in the AR-negative and HER-2-positive group.

Conclusion

In ER-negative breast cancers, AR status was associated with expression of different types of autophagy-related proteins. Tumoral LC3A was most highly expressed in AR-negative breast cancers, while tumor BNIP3 was highest in AR-positive breast cancers.     

Clinical Assessment of Lamina Cribrosa Curvature in Eyes with Primary Open-Angle Glaucoma

Purpose

Quantitative evaluation of lamina cribrosa (LC) posterior bowing in primary open-angle glaucoma (POAG) eyes using swept-source optical coherence tomography.

Methods

Patients with POAG (n = 123 eyes) and healthy individuals of a similar age (n = 92 eyes) were prospectively recruited. Anterior laminar insertion depth (ALID) was defined as the vertical distance between the anterior laminar insertion and a reference plane connecting the Bruch’s membrane openings (BMO). The mean LC depth (mLCD) was approximated by dividing the area enclosed by the anterior LC, the BMO reference plane, and the two vertical lines for ALID measurement by the length between those two vertical lines. The LC curvature index was defined as the difference between the mLCD and the ALID. The factors influencing the LC curvature index were evaluated.

Results

The ALID and mLCD were significantly larger in POAG eyes than in healthy controls (P < 0.05). The LC curvature index was significantly larger in POAG eyes than in healthy controls on both the horizontal (85.8 ± 34.1 vs. 68.2 ± 32.3 μm) and vertical meridians (49.8 ± 38.5 vs. 32.2 ± 31.1 μm, all P < 0.001). Multivariate regression showed significant associations of greater disc area (P < 0.001), vertical C/D ratio (P < 0.001) and mLCD (P < 0.001), smaller rim area (P = 0.001), thinner average RNFLT (P < 0.001), and myopic refraction (P = 0.049) with increased LC curvature index. There was no difference in the LC curvature index between mild (MD > –6 dB) and moderate-to-advanced glaucoma (MD < –6 dB, P = 0.95).

Conclusions

LC posterior bowing was increased in POAG eyes, and was significantly associated with structural optic nerve head (ONH) changes but not with functional glaucoma severity. Quantitative evaluation of LC curvature can facilitate assessment of glaucomatous ONH change.     

No Increased Risk of Herpes Zoster Found in Cirrhotic Patients: A Nationwide Population-Based Study in Taiwan

Background

The association between liver cirrhosis (LC) and herpes zoster has rarely been studied. We investigated the hypothesis that LC, known as an immunodeficiency disease, may increase the risk of herpes zoster using a national health insurance database in Taiwan.

Materials and Methods

The study cohort included cirrhotic patients between 1998 and 2005 (n = 4667), and a ratio of 1∶5 randomly sampled age- and gender-matched control patients (n = 23,335). All subjects were followed up for 5 years from the date of cohort entry to identify whether or not they had developed herpes zoster. Cox proportional-hazard regressions were performed to evaluate 5-year herpes zoster-free survival rates.

Results

Of all patients, 523 patients developed herpes zoster during the 5-year follow-up period, among whom 82 were LC patients and 441 were in the comparison cohort. The adjusted hazard ratio (AHR) of herpes zoster in patients with LC was not higher (AHR: 0.77, 95% confidence interval: 0.59–1.01, p = 0.06) than that of the controls during the 5-year follow-up. No increased risk of herpes zoster was found in LC patients after stratification by age, gender, urbanization level, income, geographic region, and all comorbidities.

Conclusions

This large nationwide population-based cohort study suggests that there is no increased risk for herpes zoster among people who have LC compared to a matching population.