Evaluation of three high abundance protein depletion kits for umbilical cord serum proteomics

<p>Abstract</p> <p>Background</p> <p>High abundance protein depletion is a major challenge in the study of serum/plasma proteomics. Prior to this study, most commercially available kits for depletion of highly abundant proteins had only been tested and evaluated in adult serum/plasma, while the depletion efficiency on umbilical cord serum/plasma had not been clarified. Structural differences between some adult and fetal proteins (such as albumin) make it likely that depletion approaches for adult and umbilical cord serum/plasma will be variable. Therefore, the primary purposes of the present study are to investigate the efficiencies of several commonly-used commercial kits during high abundance protein depletion from umbilical cord serum and to determine which kit yields the most effective and reproducible results for further proteomics research on umbilical cord serum.</p> <p>Results</p> <p>The immunoaffinity based kits (PROTIA-Sigma and 5185-Agilent) displayed higher depletion efficiency than the immobilized dye based kit (PROTBA-Sigma) in umbilical cord serum samples. Both the PROTIA-Sigma and 5185-Agilent kit maintained high depletion efficiency when used three consecutive times. Depletion by the PROTIA-Sigma Kit improved 2DE gel quality by reducing smeared bands produced by the presence of high abundance proteins and increasing the intensity of other protein spots. During image analysis using the identical detection parameters, 411 ± 18 spots were detected in crude serum gels, while 757 ± 43 spots were detected in depleted serum gels. Eight spots unique to depleted serum gels were identified by MALDI- TOF/TOF MS, seven of which were low abundance proteins.</p> <p>Conclusions</p> <p>The immunoaffinity based kits exceeded the immobilized dye based kit in high abundance protein depletion of umbilical cord serum samples and dramatically improved 2DE gel quality for detection of trace biomarkers.</p

Microstructure and structural modulation of lutetium dihydride LuH2 as seen via transmission electron microscopy

Structural investigations conducted using transmission electron microscopy (TEM) on LuH2 synthesized under atmospheric pressure (AP-LuH2) and nitrogen-doped LuH2 synthesized under high pressure (HP-LuH2) have revealed numerous microstructural phenomena. Both materials show a clear superstructure modulation with wave vector, q^* = 1/4 (2-20), and this modulation can be well interpreted by the displacements of Lu atoms. Further investigations on the nitrogen-doped HP-LuH2 materials reveal the appearance of high-density antiphase boundaries, in particular, domain walls of a few atomic layer thickness without structural modulation can be observed, suggesting possible interface properties could be detected in this system. In-situ TEM observations of AP-LuH2 suggest that no evident structural phase transition occurs between 94 K and 673 K.Comment: 8 pages, 7 figure

The Ratio of Plasma and Urinary 8-oxo-Gsn Could Be a Novel Evaluation Index for Patients with Chronic Kidney Disease

Nucleic acid oxidation plays an important role in the pathophysiology progress of a variety of diseases. 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dGsn) and 8-oxo-7,8-dihydroguanosine (8-oxo-Gsn), which originate from DNA and RNA oxidation, were the most widely used indicators for oxidative stress. The study investigated the relation between 8-oxo-dGsn, 8-oxo-Gsn, and CKD. 146 patients with CKD were divided into five disease stages, and their fasting blood and morning urine were collected. The levels of 8-oxo-dGsn and 8-oxo-Gsn in plasma and urine were quantified by LC-MS/MS. The ratio of urinary 8-oxo-Gsn to creatinine increased from stages 1 to 4 corresponding to the increased severity of CKD, but it decreased in stage 5. And plasma 8-oxo-Gsn gradually increased with the decline of renal function. In particular, the increased ratio of plasma and urine 8-oxo-Gsn in stage 5 exceeded the concentration of creatinine. This trend was similar to the estimated glomerular filtration rate (eGFR), which indicates that 8-oxo-Gsn could be an appropriate indicator for renal function. Our finding indicates that as the disease progresses, RNA oxidation is increased. The significant increase in the ratio of plasma and urinary 8-oxo-Gsn is a novel evaluation index of end-stage renal disease

An atlas of DNA methylomes in porcine adipose and muscle tissues

It is evident that epigenetic factors, especially DNA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DNA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generate 1,381 Gb of sequence data from 180 methylated DNA immunoprecipitation libraries, and provide a genome-wide DNA methylation map as well as a gene expression map for adipose and muscle studies. The analysis shows global similarity and difference among breeds, sexes and anatomic locations, and identifies the differentially methylated regions. The differentially methylated regions in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth

Acupuncture for menstruation-related migraine prophylaxis:A multicenter randomized controlled trial

OBJECTIVE: The aim of this study was to evaluate the efficacy of acupuncture, an alternative medicine therapy, as a preventive treatment for menstruation-related migraine (MRM). PATIENTS AND METHODS: This was a prospective, multicenter, double-dummy, participant-blinded, randomized controlled clinical trial conducted in China between 1 April 2013, and 30 April 2014. The participants were enrolled from four study centers and randomized to into either the acupuncture group, which received 24 sessions of acupuncture at traditional acupoints plus placebo, or the medication group, which received sham acupuncture plus naproxen. The primary endpoint was change from the baseline average number of migraine days per perimenstrual period over cycles 1−3. The secondary endpoints included changes from the baseline average number of migraine days outside the perimenstrual period, mean number of migraine hours during and outside the perimenstrual period, mean visual analog scale score during and outside the perimenstrual period, ≥50% migraine responder rate, and the proportion of participants who used acute pain medication over cycles 1−3 and 4−6. RESULTS: A total of 172 women with MRM were enrolled; 170 in the intention-to-treat analyses. Our primary outcome reported a significant between-group difference that favored the acupuncture group (95% CI, 0.17–0.50; P < 0.001), with the average reduction of migraine days per perimenstrual period from the baseline was 0.94 (95% CI, 0.82–1.07) in the acupuncture group and 0.61 (95% CI, 0.50–0.71) in the medication group over cycles 1−3. CONCLUSION: This study showed that compared to medication, acupuncture reduces the number of migraine days experienced by patients with MRM. For patients who received the acupuncture treatment over three cycles, the preventive effect of the therapy was sustained for six cycles. CLINICAL TRIAL REGISTRATION: [https://www.isrctn.com/ISRCTN57133712], identifier [ISRCTN15663606]

A longitudinal resource for population neuroscience of school-age children and adolescents in China

During the past decade, cognitive neuroscience has been calling for population diversity to address the challenge of validity and generalizability, ushering in a new era of population neuroscience. The developing Chinese Color Nest Project (devCCNP, 2013–2022), the first ten-year stage of the lifespan CCNP (2013–2032), is a two-stages project focusing on brain-mind development. The project aims to create and share a large-scale, longitudinal and multimodal dataset of typically developing children and adolescents (ages 6.0–17.9 at enrolment) in the Chinese population. The devCCNP houses not only phenotypes measured by demographic, biophysical, psychological and behavioural, cognitive, affective, and ocular-tracking assessments but also neurotypes measured with magnetic resonance imaging (MRI) of brain morphometry, resting-state function, naturalistic viewing function and diffusion structure. This Data Descriptor introduces the first data release of devCCNP including a total of 864 visits from 479 participants. Herein, we provided details of the experimental design, sampling strategies, and technical validation of the devCCNP resource. We demonstrate and discuss the potential of a multicohort longitudinal design to depict normative brain growth curves from the perspective of developmental population neuroscience. The devCCNP resource is shared as part of the “Chinese Data-sharing Warehouse for In-vivo Imaging Brain” in the Chinese Color Nest Project (CCNP) – Lifespan Brain-Mind Development Data Community (https://ccnp.scidb.cn) at the Science Data Bank

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Accelerometer-Measured Physical Activity in Children and Adolescents at Altitudes over 3500 Meters: A Cross-Sectional Study in Tibet

There is a scarcity of studies on the physical activity (PA) of children and adolescents who live at high altitudes. This study aimed to objectively assess PA of children and adolescents living in the Tibet at altitudes over 3500 m and to examine its difference by ethnicity, gender, age/grade, and body weight status groups. A sample of 397 students aged 9&#8315;18 years were recruited from 7 schools in Lhasa, Tibet. PA was measured using accelerometers (ActiGraph GT3X) for seven consecutive days and moderate to vigorous PA (MVPA) was identified using the Evenson (2008) cut-points. Participant MVPA was 62.3 min/day, with 65.5 min/day during weekdays and 54.1 min/day on weekends. Indigenous Tibetans were more active than Hans, and boys had more MVPA than girls. Age had a significantly weak negative correlation with MVPA. There was no significant difference in MVPA between the non-overweight and overweight/obese groups. Overall, only 9.1% (13.8% in boys and 4.5% in girls) accumulated at least 60 min of MVPA per day. Compared to their counterparts in other regions, the daily MVPA of children and adolescents living on the Tibetan Plateau at altitudes over 3500 m was relatively high. However, the proportion of meeting the WHO&#8217;s PA recommendations was extremely low

Lower Expression of SLC27A1 Enhances Intramuscular Fat Deposition in Chicken via Down-Regulated Fatty Acid Oxidation Mediated by CPT1A

Intramuscular fat (IMF) is recognized as the predominant factor affecting meat quality due to its positive correlation with tenderness, juiciness, and flavor. Chicken IMF deposition depends on the balance among lipid synthesis, transport, uptake, and subsequent metabolism, involving a lot of genes and pathways, however, its precise molecular mechanisms remain poorly understood. In the present study, the breast muscle tissue of female Wenchang chickens (WC) (higher IMF content, 1.24 in D120 and 1.62 in D180) and female White Recessive Rock chickens (WRR; lower IMF content, 0.53 in D120 and 0.90 in D180) were subjected to RNA-sequencing (RNA-seq) analysis. Results showed that many genes related to lipid catabolism, such as SLC27A1, LPL, ABCA1, and CPT1A were down-regulated in WC chickens, and these genes were involved in the PPAR signaling pathway and formed an IPA® network related to lipid metabolism. Furthermore, SLC27A1 was more down-regulated in WRR.D180.B than in WRR.D120.B. Decreased cellular triglyceride (TG) and up-regulated CPT1A were observed in the SLC27A1 overexpression QM-7 cells, and increased cellular triglyceride (TG) and down-regulated CPT1A were observed in the SLC27A1 knockdown QM-7 cells. These results suggest that lower lipid catabolism exists in WC chickens but not in WRR chickens, and lower expression of SLC27A1 facilitate IMF deposition in chicken via down-regulated fatty acid oxidation mediated by CPT1A. These findings indicate that reduced lipid catabolism, rather than increased lipid anabolism, contributes to chicken IMF deposition