Genetic polymorphism of erythrocyte diaphorase in red deer, Cervus elaphus L.

NADH diaphorase polymorphism was identified in red deer erythrocyte lysates using starch gel electrophoresis and activity staining. The inheritance of the polymorphism was consistent with predictions of autosomal codominant inheritance of two alleles DIA1F and DIAS. In New Zealand's four main feral red deer populations (n = 188) the DIA1F allele frequency ranged from 0.491 to 0.985. A sample of North American wapiti (n = 42) was monomorphic for the DIA1F allele.     

Diaphragm, genioglossus, and triangularis sterni responses to poikilocapnic hypoxia

Both isocapnic and poikilocapnic hypoxia may elicit a biphasic respiratory response, during which an initial ventilatory stimulation is followed by a reduction in breathing and diaphragm (DIA) electrical activity. To ascertain whether during adulthood other respiratory muscles have biphasic hypoxic responses similar to the DIA, in nine anesthetized cats electromyograms (EMG) were recorded from the DIA, genioglossus (GG), and triangularis sterni (TS) (n = 7) muscles during poikilocapnic hypoxia. DIA and GG EMG started at 60 +/- 4 and 9 +/- 3 units, respectively, during O2 breathing, increased to a maximum of 100 units during the 10-min hypoxic stimulus, and subsequently declined to 81 +/- 6 and 58 +/- 12 units, respectively, by the end of 10 min of hypoxia. The time course of the increase and subsequent decline was similar for the DIA and GG and for GG activity during both inspiration and expiration. Furthermore the degree to which GG EMG declined after reaching its peak activity level correlated with the magnitude of the respective decline in DIA EMG (r = 0.79, P less than 0.02). The TS, in contrast, was maximally active either during O2 breathing or very early during hypoxia, and its activity declined progressively thereafter (to 13 +/- 6% of its peak value at the end of 10 min of hypoxia). The degree to which TS EMG declined did not correlate with the degree to which DIA or GG EMG declined.(ABSTRACT TRUNCATED AT 250 WORDS)     

DIA1R is an X-linked gene related to Deleted In Autism-1

Background

Autism spectrum disorders (ASDs) are frequently occurring disorders diagnosed by deficits in three core functional areas: social skills, communication, and behaviours and/or interests. Mental retardation frequently accompanies the most severe forms of ASDs, while overall ASDs are more commonly diagnosed in males. Most ASDs have a genetic origin and one gene recently implicated in the etiology of autism is the Deleted-In-Autism-1 (DIA1) gene.

Methodology/Principal Findings

Using a bioinformatics-based approach, we have identified a human gene closely related to DIA1, we term DIA1R (DIA1-Related). While DIA1 is autosomal (chromosome 3, position 3q24), DIA1R localizes to the X chromosome at position Xp11.3 and is known to escape X-inactivation. The gene products are of similar size, with DIA1 encoding 430, and DIA1R 433, residues. At the amino acid level, DIA1 and DIA1R are 62% similar overall (28% identical), and both encode signal peptides for targeting to the secretory pathway. Both genes are ubiquitously expressed, including in fetal and adult brain tissue.

Conclusions/Significance

Examination of published literature revealed point mutations in DIA1R are associated with X-linked mental retardation (XLMR) and DIA1R deletion is associated with syndromes with ASD-like traits and/or XLMR. Together, these results support a model where the DIA1 and DIA1R gene products regulate molecular traffic through the cellular secretory pathway or affect the function of secreted factors, and functional deficits cause disorders with ASD-like symptoms and/or mental retardation.     

A Comparison of Visual Assessment and Automated Digital Image Analysis of Ki67 Labeling Index in Breast Cancer

Background

Ki67 labeling index (LI) is critical for treatment options and prognosis evaluation in breast cancer. Visual assessment (VA) is widely used to assess Ki67 LI, but has some limitations. In this study, we compared the consistency between VA and automated digital image analysis (DIA) of Ki67 LI in breast cancer, and to evaluate the application value of DIA in Ki67 LI assessment.

Methods

Ki67 immunostained slides of 155 cases of primary invasive breast cancer were eyeballing assessed by five breast pathologists and automated digital image analyzed by one breast pathologist respectively. Two score methods, hot-spot score and average score, were used to choose score areas. The intra-class correlation coefficient (ICC) was used to analyze the consistency between VA and DIA, and Wilcoxon signed-rank test was used to compare the median of paired-difference between VA and DIA values.

Results

(1) A perfect agreement was demonstrated between VA and DIA of Ki67 LI by ICC analysis (P<0.0001) in the whole cohort. A perfect agreement between VA and DIA of Ki67 LI was also showed in G2-G3, ER positive/HER2 negative cases. Average score and hot-spot score methods both demonstrated a perfect concordance between VA and DIA of Ki67 LI. (2) All cases were classified into three groups by VA values (≤10%, 11%-30% and >30% Ki67 LI). The concordance was relatively lower in intermediate Ki67 LI group (11%-30%) compared with high (>30%) Ki67 LI groups according to both methods. (3) All cases were classified into three groups by paired-difference (d) between VA values of hot-spot score and average score (d<5, 5≤d<10, d≥10) to evaluate the correlation between Ki67 staining distribution (heterogeneous or homogenous) and reproducibility of assessment. A perfect agreement was all demonstrated in three groups, and a slightly better Ki67 LI agreement between VA and DIA was indicated in homogenous staining slides than in heterogeneous staining ones. (4) VA values were relatively smaller than DIA values (average score: median of paired-difference -3.72; hot-spot score: median of paired-difference -9.12).

Conclusions

An excellent agreement between VA and DIA of Ki67 LI in breast cancer was demonstrated in the whole mixed cohort, suggesting that VA and DIA both could be used to assess Ki67 LI in clinical practice. Average score and hot-spot score methods both demonstrated a perfect concordance between VA and DIA of Ki67 LI. The almost perfect agreement between VA and DIA was observed in high Ki67 LI cases, displaying a homogenous staining pattern. The consistency between VA and DIA was relatively low in intermediate Ki67 LI group. The heterogeneity of tumors may slightly affect the concordance between VA and DIA of Ki67 LI. Assessment of VA provides lower Ki67 values than DIA, the biological importance of these values are not known at the moment.     

Characterization of the deleted in autism 1 protein family: implications for studying cognitive disorders

Autism spectrum disorders (ASDs) are a group of commonly occurring, highly-heritable developmental disabilities. Human genes c3orf58 or Deleted In Autism-1 (DIA1) and cXorf36 or Deleted in Autism-1 Related (DIA1R) are implicated in ASD and mental retardation. Both gene products encode signal peptides for targeting to the secretory pathway. As evolutionary medicine has emerged as a key tool for understanding increasing numbers of human diseases, we have used an evolutionary approach to study DIA1 and DIA1R. We found DIA1 conserved from cnidarians to humans, indicating DIA1 evolution coincided with the development of the first primitive synapses. Nematodes lack a DIA1 homologue, indicating Caenorhabditis elegans is not suitable for studying all aspects of ASD etiology, while zebrafish encode two DIA1 paralogues. By contrast to DIA1, DIA1R was found exclusively in vertebrates, with an origin coinciding with the whole-genome duplication events occurring early in the vertebrate lineage, and the evolution of the more complex vertebrate nervous system. Strikingly, DIA1R was present in schooling fish but absent in fish that have adopted a more solitary lifestyle. An additional DIA1-related gene we named DIA1-Like (DIA1L), lacks a signal peptide and is restricted to the genomes of the echinoderm Strongylocentrotus purpuratus and cephalochordate Branchiostoma floridae. Evidence for remarkable DIA1L gene expansion was found in B. floridae. Amino acid alignments of DIA1 family gene products revealed a potential Golgi-retention motif and a number of conserved motifs with unknown function. Furthermore, a glycine and three cysteine residues were absolutely conserved in all DIA1-family proteins, indicating a critical role in protein structure and/or function. We have therefore identified a new metazoan protein family, the DIA1-family, and understanding the biological roles of DIA1-family members will have implications for our understanding of autism and mental retardation.     

Mitochondrial capacity is affected by glycemic status in young untrained women with type 1 diabetes but is not impaired relative to healthy untrained women

In this study, we examined whether glycemic status influences aerobic function in women with type 1 diabetes and whether aerobic function is reduced relative to healthy women. To this end, we compared several factors determining aerobic function of 29 young sedentary asymptomatic women (CON) with 9 women of similar age and activity level with type 1 diabetes [DIA, HbA1c range = 6.9-8.2%]. Calf muscle mitochondrial capacity was estimated by (31)P-magnetic resonance spectroscopy. Capillarization and muscle fiber oxidative enzyme activity were assessed from vastus lateralis and soleus muscle biopsies. Oxygen uptake and cardiac output were evaluated by ergospirometry and N(2)O/SF(6) rebreathing. Calf muscle mitochondrial capacity was not different between CON and DIA, as indicated by the identical calculated maximal rates of oxidative ATP synthesis [0.0307 (0.0070) vs. 0.0309 (0.0058) s(-1), P = 0.930]. Notably, HbA1c was negatively correlated with mitochondrial capacity in DIA (R(2) = 0.475, P = 0.040). Although HbA1c was negatively correlated with cardiac output (R(2) = 0.742, P = 0.013) in DIA, there was no difference between CON and DIA in maximal oxygen consumption [2.17 (0.34) vs. 2.21 (0.32) l/min, P = 0.764], cardiac output [12.1 (1.9) vs. 12.3 (1.8) l/min, P = 0.783], and endurance capacity [532 (212) vs. 471 (119) s, P = 0.475]. There was also no difference between the two groups either in the oxidative enzyme activity or capillary-to-fiber ratio. We conclude that mitochondrial capacity depends on HbA1c in untrained women with type 1 diabetes but is not reduced relative to untrained healthy women.     

Reliability of computerized image analysis for the evaluation of serial synovial biopsies in randomized controlled trials in rheumatoid arthritis

Analysis of biomarkers in synovial tissue is increasingly used in the evaluation of new targeted therapies for patients with rheumatoid arthritis (RA). This study determined the intrarater and inter-rater reliability of digital image analysis (DIA) of synovial biopsies from RA patients participating in clinical trials. Arthroscopic synovial biopsies were obtained before and after treatment from 19 RA patients participating in a randomized controlled trial with prednisolone. Immunohistochemistry was used to detect CD3⁺ T cells, CD38⁺ plasma cells and CD68⁺ macrophages. The mean change in positive cells per square millimetre for each marker was determined by different operators and at different times using DIA. Nonparametric tests were used to determine differences between observers and assessments, and to determine changes after treatment. The intraclass correlations (ICCs) were calculated to determine the intrarater and inter-rater reliability. Intrarater ICCs showed good reliability for measuring changes in T lymphocytes (R = 0.87), plasma cells (R = 0.62) and macrophages (R = 0.73). Analysis by Bland–Altman plots showed no systemic differences between measurements. The smallest detectable changes were calculated and their discriminatory power revealed good response in the prednisolone group compared with the placebo group. Similarly, inter-rater ICCs also revealed good reliability for measuring T lymphocytes (R = 0.68), plasma cells (R = 0.69) and macrophages (R = 0.72). All measurements identified the same cell types as changing significantly in the treated patients compared with the placebo group. The measurement of change in total positive cell numbers in synovial tissue can be determined reproducibly for various cell types by DIA in RA clinical trials.     

Dioxindole-3-Acetic Acid Conjugates Formation from Indole-3-Acetylaspartic Acid in Vicia Seedlings

When indole-3-acetic acid (IAA) is applied to the cotyledonsof broad bean seedlings (Vicia faba L. cv Chukyo), the majormetabolites found in the roots are 3-(O-ß-glucosyl)-2-indoIone-3-acetylaspartic acid (Glc-DIA-Asp) and 3-hydroxy-2-indolone-3-acetylasparticacid (DIA-Asp). In this report, the metabolic pathway from IAAto the two dioxindole-3-acetic acid (DIA) conjugates was investigatedby using [¹⁴C]IAA, [¹⁴C]DIA, [¹⁴C]indole-3-acetylaspartic acid(IAA-Asp), and [¹⁴C]IAA-[³H]Asp. The precursor of DIA-Asp wasfound to be IAA-Asp but not DIA. Incorporation of the doublelabeled IAA-Asp into the DIA conjugates demonstrated that hydrolysisof IAA-Asp was not involved in the formation of the DIA conjugates.DIA-Asp was further metabolized to Glc-DIA-Asp in the cotyledons,while formation of Glc-DIA-Asp in the roots was very low. Glc-DIA-Aspformed in the cotyledons was transported to the roots. (Received April 21, 1986; Accepted September 10, 1986)     

Developmental changes in sequential activation of laryngeal abductor muscle and diaphragm in infants.

In animals and human adults, upper airway muscle activity usually precedes inspiratory diaphragm activity. We examined the interaction of the posterior cricoarytenoid muscle (PCA), which abducts the larynx, and the diaphragm (DIA) in the control of airflow in newborn infants to assess the effect of maturation on respiratory muscle sequence. We recorded tidal volume, airflow, and DIA and PCA electromyograms (EMG) in 12 full-term, 14 premature, and 10 premature infants with apnea treated with aminophylline. In most breaths, onset of PCA EMG activity preceded onset of DIA EMG activity (lead breaths). In all subjects, we also observed breaths (range 6-61%) in which PCA EMG onset followed DIA EMG onset (lag breaths). DIA neural inspiratory duration and the neuromechanical delay between DIA EMG onset and inspiratory flow were longer in lag than in lead breaths (P < 0.05 and P < 0.01, respectively). The frequency of lag breaths was greater in the premature infants [33 +/- 4% (SE)] than in either the full-term infants (21 +/- 3%, P < 0.03) or the premature infants with apnea treated with aminophylline (16 +/- 2%, P < 0.01). We conclude that the expected sequence of onset of PCA and DIA EMG activity is frequently disrupted in newborn infants. Both maturation and respiratory stimulation with aminophylline improve the coordination of the PCA and DIA.     

Digital immunohistochemistry wizard: image analysis-assisted stereology tool to produce reference data set for calibration and quality control

Background

Digital image analysis (DIA) enables better reproducibility of immunohistochemistry (IHC) studies. Nevertheless, accuracy of the DIA methods needs to be ensured, demanding production of reference data sets. We have reported on methodology to calibrate DIA for Ki67 IHC in breast cancer tissue based on reference data obtained by stereology grid count. To produce the reference data more efficiently, we propose digital IHC wizard generating initial cell marks to be verified by experts.

Methods

Digital images of proliferation marker Ki67 IHC from 158 patients (one tissue microarray spot per patient) with an invasive ductal carcinoma of the breast were used. Manual data (mD) were obtained by marking Ki67-positive and negative tumour cells, using a stereological method for 2D object enumeration. DIA was used as an initial step in stereology grid count to generate the digital data (dD) marks by Aperio Genie and Nuclear algorithms. The dD were collected into XML files from the DIA markup images and overlaid on the original spots along with the stereology grid. The expert correction of the dD marks resulted in corrected data (cD). The percentages of Ki67 positive tumour cells per spot in the mD, dD, and cD sets were compared by single linear regression analysis. Efficiency of cD production was estimated based on manual editing effort.

Results

The percentage of Ki67-positive tumor cells was in very good agreement in the mD, dD, and cD sets: regression of cD from dD (R²=0.92) reflects the impact of the expert editing the dD as well as accuracy of the DIA used; regression of the cD from the mD (R²=0.94) represents the consistency of the DIA-assisted ground truth (cD) with the manual procedure. Nevertheless, the accuracy of detection of individual tumour cells was much lower: in average, 18 and 219 marks per spot were edited due to the Genie and Nuclear algorithm errors, respectively. The DIA-assisted cD production in our experiment saved approximately 2/3 of manual marking.

Conclusions

Digital IHC wizard enabled DIA-assisted stereology to produce reference data in a consistent and efficient way. It can provide quality control measure for appraising accuracy of the DIA steps.

     

Exercise training protects against contraction-induced lipid peroxidation in the diaphragm

Endurance exercise training promotes a small but significant increase in antioxidant enzyme activity in the costal diaphragm (DIA) of rodents. It is unclear if these training-induced improvements in muscle antioxidant capacity are large enough to reduce oxidative stress during prolonged contractile activity. To test the hypothesis that training-related increases in DIA antioxidant capacity reduces contraction-induced lipid peroxidation, we exercise trained adult female Sprague-Dawley (n = 7) rats on a motor-driven treadmill for 12 weeks at approximately 75% maximal O2 consumption (90 min/day). Control animals (n = 8) remained sedentary during the same 12-week period. After training, DIA strips from animals in both experimental groups were excised and subjected to an in vitro fatigue contractile protocol in which the muscle was stimulated for 60 min at a frequency of 30 Hz, every 2 s, with a train duration of 330 m. Compared to the controls, endurance training resulted in an increase (P < 0.05) in diaphragmatic non-protein thiols and in the activity of the antioxidant enzyme superoxide dismutase. Following the contractile protocol, lipid peroxidation was significantly lower (P < 0.05) in the trained DIA compared to the controls. These data support the hypothesis that endurance exercise training-induced increases in DIA antioxidant capacity protect the muscle against contractile-related oxidative stress.     

New targeted approaches for the quantification of data‐independent acquisition mass spectrometry

The use of data‐independent acquisition (DIA) approaches for the reproducible and precise quantification of complex protein samples has increased in the last years. The protein information arising from DIA analysis is stored in digital protein maps (DIA maps) that can be interrogated in a targeted way by using ad hoc or publically available peptide spectral libraries generated on the same sample species as for the generation of the DIA maps. The restricted availability of certain difficult‐to‐obtain human tissues (i.e., brain) together with the caveats of using spectral libraries generated under variable experimental conditions limits the potential of DIA. Therefore, DIA workflows would benefit from high‐quality and extended spectral libraries that could be generated without the need of using valuable samples for library production. We describe here two new targeted approaches, using either classical data‐dependent acquisition repositories (not specifically built for DIA) or ad hoc mouse spectral libraries, which enable the profiling of human brain DIA data set. The comparison of our results to both the most extended publically available human spectral library and to a state‐of‐the‐art untargeted method supports the use of these new strategies to improve future DIA profiling efforts.     

Data‐Independent Acquisition Mass Spectrometry‐Based Proteomics and Software Tools: A Glimpse in 2020

This review provides a brief overview of the development of data‐independent acquisition (DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various DIA acquisition schemes for proteomics are summarized first including Shotgun‐CID, DIA, MS^E, PAcIFIC, AIF, SWATH, MSX, SONAR, WiSIM, BoxCar, Scanning SWATH, diaPASEF, and PulseDIA, as well as the mass spectrometers enabling these methods. Next, the software tools for DIA data analysis are classified into three groups: library‐based tools, library‐free tools, and statistical validation tools. The approaches are reviewed for generating spectral libraries for six selected library‐based DIA data analysis software tools which are tested by the authors, including OpenSWATH, Spectronaut, Skyline, PeakView, DIA‐NN, and EncyclopeDIA. An increasing number of library‐free DIA data analysis tools are developed including DIA‐Umpire, Group‐DIA, PECAN, PEAKS, which facilitate identification of novel proteoforms. The authors share their user experience of when to use DIA‐MS, and several selected DIA data analysis software tools. Finally, the state of the art DIA mass spectrometry and software tools, and the authors’ views of future directions are summarized.     

Tumor necrosis factor-alpha and malnutrition-induced inhibition of diaphragm fiber growth in young rats.

Tumor necrosis factor (TNF)-alpha has been implicated in several muscle-wasting disorders, with increased levels of the cytokine reported in malnourished children. The role of TNF-alpha in mediating malnutrition-induced inhibition of diaphragm (DIA) muscle growth in young growing rats was evaluated. Three groups of rats were studied: 1) control (CTL); 2) nutritional deprivation (ND; 50% of normal food intake for 7 days); and 3) ND + rat specific anti-TNF-alpha antibody. DIA fiber cross-sectional areas were determined. Serum and muscle TNF-alpha levels were measured by real-time PCR, ELISA, and immunohistochemistry. Body weights decreased 20% in ND rats and increased 46% in CTL animals. Anti-TNF-alpha had no effect on body weight or on DIA mass in ND animals. ND significantly reduced cross-sectional areas of all fiber types (33-46%). Anti-TNF-alpha failed to attenuate ND-induced inhibition of DIA fiber growth. Serum TNF-alpha levels increased 2.6-fold in ND animals, with levels suppressed to below CTL values with anti-TNF-alpha. DIA TNF-alpha mRNA and protein levels increased two- to threefold in ND rats. Anti-TNF-alpha antibodies suppressed muscle levels of the cytokine in ND animals to near CTL values. TNF-alpha immunoreactivity in all DIA fibers revealed similar directions of change in both ND groups. Direction and magnitude of change in DIA phosphorylated p38 MAPK (a likely second messenger of TNF-alpha) tracked those of TNF-alpha. Muscle levels of IGF-I mRNA and phosphorylated Akt were markedly reduced in ND animals with no change following anti-TNF-alpha therapy. Thus rat anti-TNF-alpha at a dose known to neutralize the cytokine failed to attenuate or reverse ND-induced inhibition of DIA fiber growth in our model.     

Course of liver regeneration after partial hepatectomy in rats treated with dialysates obtained 17 hours after partial hepatectomy

Various theories have been put forward to explain the regenerative capacity of liver tissue induce by partial hepatectomy (PH). One of them presumes the existence of humoral factors stimulating proliferation of the liver tissue. We evaluated the course of liver regeneration after 65-70% PH as influenced by dialysates (DIA) of the organs of a rat killed 17 h after PH. In addition to kidney DIA, we were particularly interested in the effect of liver and spleen DIA. The experiments were carried out on rats weighting 310-370 g. Kidney, liver or spleen dialysate was administered subcutaneously and the rats were killed 12 or 24 h later by exsanguination from the abdominal aorta. In further rats, PH was performed 24 h after administering DIA and the rat were killed 18, 24, 30, 48 and 72 h after the operation. The initiation of liver regeneration was stimulated by all the given DIA, but especially by liver DIA. The faster onset of liver regeneration 18 h after PH in rats given spleen DIA is interesting. DIA did not greatly affect the hepatocytes of intact liver, but accelerated the initiation of liver regeneration after PH by synchronizing the cell cycle of proliferating hepatocytes. DIA obtained 17 h after PH contained substances which primarily stimulated liver DNA synthesis. From the changes in inhibition of the migration of spleen macrophages in the medium containing liver antigens, and from the circulating immunocomplex values, we conclude that DIA activation of the immune system, a well as the hepatic stimulator substance contained in the DIA, participates in acceleration of the liver regeneration process.     

Insulin-like growth factor I prevents corticosteroid-induced diaphragm muscle atrophy in emphysematous hamsters

The aim of this study was to evaluate whether recombinant human insulin-like growth factor I (rhIGF-I) could attenuate or prevent diaphragm (DIA) fiber atrophy with corticosteroid (CS) administration to emphysematous (EMP) hamsters. DIA muscle IGF-I responses to CS administration with and without exogenous rhIGF-I administration were evaluated. Three groups were studied: 1) EMP; 2) EMP + triamcinolone (T; 0.4 mg.kg-1.day-1 im); and 3) EMP + T + IGF-I (600 microg/day by constant infusion). After 4 wk, the DIA was analyzed histochemically and biochemically (IGF-I mRNA levels by RT-PCR and endogenous and exogenous IGF-I peptide levels immunochemically). Body weights of EMP-T progressively decreased, while those of EMP and EMP-T-IGF-I remained stable despite similarly reduced food intake in both T groups. DIA weight was reduced with T but preserved with rhIGF-I infusion. DIA fiber proportions were similar among the groups. The cross-sectional areas of types I, IIa, and IIx fibers were reduced (17 to 31%) with T administration but unchanged with rhIGF-I infusion. DIA IGF-I mRNA levels were similar across all groups. By contrast, the endogenous DIA IGF-I levels were reduced (41%) in the EMP-T-IGF-I animals. Total DIA IGF-I levels (endogenous + exogenous) were still significantly reduced. IGF-I immunoreactivity confirmed this reduction in all DIA fibers. We conclude that DIA fiber atrophy with T was completely prevented by exogenous rhIGF-I administration. This effect was likely mediated by the pharmacological influences of exogenously administered rhIGF-I. We speculate that this results from increased bioavailability of free IGF-I to react with muscle receptors. Reduced endogenous IGF-I levels in the DIA likely reflect a negative-feedback influence. These results may have important clinical implications for treatment options to offset the adverse effects of CS on the respiratory muscles in patients with chronic lung disorders.     

Distribution of human Zn-alpha-2-glycoprotein types in Chinese and Korean populations

The genetic variation in Zn-alpha 2-glycoprotein (ZAG) was investigated by polyacrylamide gel isoelectric focusing and immunoblotting. The samples comprised 590 Chinese from 2 localities (Shenyang: n = 390; Kaohsiung: n = 200) and 873 Koreans from 2 localities (Seoul: n = 523; Cheju: n = 350). The allele frequencies were: ZAG*1 = 0.9962, ZAG*5 = 0.0038 in Shenyang; ZAG*1 = 1.0000 in Kaohsiung; ZAG*1 = 0.9971, ZAG*3 = 0.0029 in Seoul, and ZAG*1 = 0.9929, ZAG*3 = 0.0071 in Cheju.     

Contractile properties of the rat external abdominal oblique and diaphragm muscles during development.

We studied the in vitro contractile and fatigue properties of the rat external abdominal oblique (EAO) and costal diaphragm (DIA) muscles during postnatal development. Isometric twitch contraction (CT) and half-relaxation (RT1/2) times were longer in both the EAO and DIA muscles during the early postnatal period and decreased with age. In the first postnatal week, the CT and RT1/2 were longer in the EAO than the DIA muscle. At 14 days of age and thereafter, the CT and RT1/2 were shorter in the EAO than in the DIA muscle. Force-frequency relationships of the EAO and DIA muscles changed during postnatal development such that the relative force (percent maximum) generated at lower frequencies (less than 15 pulses/s) decreased with age. Moreover the relative force generated by the EAO muscle at lower frequencies was greater than that of the DIA muscle during the early postnatal period but less than that of the DIA muscle in adults. The specific force of both the EAO and DIA muscles increased progressively with age. There were no differences in specific force between the EAO and DIA muscles at any age. The fatigability of the EAO and DIA muscles was comparable during the early postnatal period and increased in both muscles with postnatal development. In adults the EAO muscle was more fatigable than the DIA muscle. We conclude that the contractile and fatigue properties of the EAO and DIA muscles undergo significantly different postnatal transitions, which may reflect their functional involvement in sustaining ventilation.     

Histochemical characteristics of human expiratory and inspiratory intercostal muscles

The relative occurrence of slow-twitch (ST) and fast-twitch (FTa and FTb) fibers, fiber size, and capillary supply in internal (INT) and external intercostal muscles (EXT), the costal diaphragm (DIA), and vastus lateralis muscle (VAS) was examined post-mortem in eight healthy males. The relative occurrence of ST fibers in INT [64 +/- 3% (SE)] and EXT (62 +/- 3%) was similar but higher than in DIA (49 +/- 3%) and VAS (40 +/- 6%; P less than 0.05). The occurrence of FTa fibers in expiratory INT (35 +/- 3%) was higher than in inspiratory INT and EXT (17 +/- 1%; P less than 0.05) but similar to DIA (28 +/- 6%) and VAS (32 +/- 2%). Accordingly, expiratory INT had fewer FTb fibers (1 +/- 1%) than the others (P less than 0.05). Expiratory INT had a 60% larger fiber area than inspiratory INT and EXT and DIA (P less than 0.05), but the area was similar to that of VAS. The number of capillaries per fiber was higher in expiratory INT (2.3 +/- 0.1) than in inspiratory INT and EXT (1.6 +/- 0.1), DIA (1.9 +/- 0.1), and VAS (1.8 +/- 0.2; P less than 0.05). The results suggest that the occurrence of many large capillary-rich FTa fibers in expiratory INT is bound to function (expiratory vs. inspiratory) rather than to anatomy (INT vs. EXT).     

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries

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Highlights

• •Rapid DIA-only library building with gas-phase fractionation.
• •Recommended DIA acquisition strategies with staggered windows and forbidden zones.
• •Optimized DIA instrument settings for several Thermo Orbitrap instruments.
• •Data analysis tutorial using open source DIA software.