Mechanism of autocatalytic activation during proteasome assembly

Many large molecular machines are too elaborate to assemble spontaneously and are built through ordered pathways orchestrated by dedicated chaperones. During assembly of the core particle (CP) of the proteasome, where protein degradation occurs, its six active sites are simultaneously activated via cleavage of N-terminal propeptides. Such activation is autocatalytic and coupled to fusion of two half-CP intermediates, which protects cells by preventing activation until enclosure of the active sites within the CP interior. Here we uncover key mechanistic aspects of autocatalytic activation, which proceeds through alignment of the β5 and β2 catalytic triad residues, respectively, with these triads being misaligned before fusion. This mechanism contrasts with most other zymogens, in which catalytic centers are preformed. Our data also clarify the mechanism by which individual subunits can be added in a precise, temporally ordered manner. This work informs two decades-old mysteries in the proteasome field, with broader implications for protease biology and multisubunit complex assembly.

DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples

Protein-protein interactions (PPIs) are fundamental to understanding biological systems as protein complexes are the active molecular modules critical for carrying out cellular functions. Dysfunctional PPIs have been associated with various diseases including cancer. Systems-wide PPI analysis not only sheds light on pathological mechanisms, but also represents a paradigm in identifying potential therapeutic targets. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for defining endogenous PPIs of cellular networks. While proteome-wide studies have been performed in cell lysates, intact cells and tissues, applications of XL-MS in clinical samples have not been reported. In this study, we adopted a DSBSO-based in vivo XL-MS platform to map interaction landscapes from two breast cancer patient-derived xenograft (PDX) models. As a result, we have generated a PDX interaction network comprising 2,557 human proteins and identified interactions unique to breast cancer subtypes. Interestingly, most of the observed differences in PPIs correlated well with protein abundance changes determined by TMT-based proteome quantitation. Collectively, this work has demonstrated the feasibility of XL-MS analysis in clinical samples, and established an analytical workflow for tissue cross-linking that can be generalized for mapping PPIs from patient samples in the future to dissect disease-relevant cellular networks.

Mapping Pregnancy-dependent Sulfhydrome Unfolds Diverse Functions of Protein Sulfhydration in Human Uterine Artery

Uterine artery (UA) hydrogen sulfide (H2S) production is augmented in pregnancy and, on stimulation by systemic/local vasodilators, contributes to pregnancy-dependent uterine vasodilation; however, how H2S exploits this role is largely unknown. S-sulfhydration converts free thiols to persulfides at reactive cysteine(s) on targeted proteins to affect the entire proteome posttranslationally, representing the main route for H2S to elicit its function. Here, we used Tag-Switch to quantify changes in sulfhydrated (SSH-) proteins (ie, sulfhydrome) in H2S-treated nonpregnant and pregnant human UA. We further used the low-pH quantitative thiol reactivity profiling platform by which paired sulfhydromes were subjected to liquid chromatography tandem mass spectrometry-based peptide sequencing to generate site (cysteine)-specific pregnancy-dependent H2S-responsive human UA sulfhydrome. Total levels of sulfhydrated proteins were significantly greater in pregnant vs nonpregnant human UA and further stimulated by treatment with sodium hydrosulfide. We identified a total of 360 and 1671 SSH-peptides from 480 and 1186 SSH-proteins in untreated and sodium hydrosulfide-treated human UA, respectively. Bioinformatics analyses identified pregnancy-dependent H2S-responsive human UA SSH peptides/proteins, which were categorized to various molecular functions, pathways, and biological processes, especially vascular smooth muscle contraction/relaxation. Pregnancy-dependent changes in these proteins were rectified by immunoblotting of the Tag-Switch labeled SSH proteins. Low-pH quantitative thiol reactivity profiling failed to identify low abundance SSH proteins such as KATP channels in human UA; however, immunoblotting of Tag-Switch-labeled SSH proteins identified pregnancy-dependent upregulation of SSH-KATP channels without altering their total proteins. Thus, comprehensive analyses of human UA sulfhydromes influenced by endogenous and exogenous H2S inform novel roles of protein sulfhydration in uterine hemodynamics regulation.

Exploring an Alternative Cysteine-Reactive Chemistry to Enable Proteome-Wide PPI Analysis by Cross-Linking Mass Spectrometry

The development of MS-cleavable cross-linking mass spectrometry (XL-MS) has enabled the effective capture and identification of endogenous protein-protein interactions (PPIs) and their residue contacts at the global scale without cell engineering. So far, only lysine-reactive cross-linkers have been successfully applied for proteome-wide PPI profiling. However, lysine cross-linkers alone cannot uncover the complete PPI map in cells. Previously, we have developed a maleimide-based cysteine-reactive MS-cleavable cross-linker (bismaleimide sulfoxide (BMSO)) that is effective for mapping PPIs of protein complexes to yield interaction contacts complementary to lysine-reactive reagents. While successful, the hydrolysis and limited selectivity of maleimides at physiological pH make their applications in proteome-wide XL-MS challenging. To enable global PPI mapping, we have explored an alternative cysteine-labeling chemistry and thus designed and synthesized a sulfoxide-containing MS-cleavable haloacetamide-based cross-linker, Dibromoacetamide sulfoxide (DBrASO). Our results have demonstrated that DBrASO cross-linked peptides display the same fragmentation characteristics as other sulfoxide-containing MS-cleavable cross-linkers, permitting their unambiguous identification by MSⁿ. In combination with a newly developed two-dimensional peptide fractionation method, we have successfully performed DBrASO-based XL-MS analysis of HEK293 cell lysates and demonstrated its capability to complement lysine-reactive reagents and expand PPI coverage at the systems-level.

Two-Dimensional Fractionation Method for Proteome-Wide Cross-Linking Mass Spectrometry Analysis

Cross-linking mass spectrometry (XL-MS) is an emergent technology for studying protein-protein interactions (PPIs) and elucidating architectures of protein complexes. The development of various MS-cleavable cross-linkers has facilitated the identification of cross-linked peptides, enabling XL-MS studies at the systems level. However, the scope and depth of cellular networks revealed by current XL-MS technologies remain limited. Due to the inherently broad dynamic range and complexity of proteomes, interference from highly abundant proteins impedes the identification of low-abundance cross-linked peptides in complex samples. Thus, peptide enrichment prior to MS analysis is necessary to enhance cross-link identification for proteome-wide studies. Although chromatographic techniques including size exclusion (SEC) and strong cation exchange (SCX) have been successful in isolating cross-linked peptides, new fractionation methods are still needed to further improve the depth of PPI mapping. Here, we present a two-dimensional (2D) separation strategy by integrating peptide SEC with tip-based high pH reverse-phase (HpHt) fractionation to expand the coverage of proteome-wide XL-MS analyses. Combined with the MS-cleavable cross-linker DSSO, we have successfully mapped in vitro PPIs from HEK293 cell lysates with improved identification of cross-linked peptides compared to existing approaches. The method developed here is effective and can be generalized for cross-linking studies of complex samples.

A new urinary exosome enrichment method by a combination of ultrafiltration and TiO2 nanoparticles

Exosomes are small membrane-bound vesicles secreted by most cell types and play an important role in cell-to-cell communication. Increasing evidence shows that exosomal proteins in urine may be used as novel biomarkers for certain diseases. Purified urinary exosomes are necessary for downstream studies and application development. However, conventional methods for exosome isolation and enrichment are technically challenging and time-consuming. Poor specificity, low recovery and instrumental dependence also limit the use of these methods. It is particularly urgent to develop a rapid and efficient extraction method for basic research and clinical application. Particularly, urine is a dilute solution system with relatively low abundance of exosomes, due to which the isolation of urinary exosome requires more efficient technology. Here, we propose a new strategy for facile exosome isolation from human urine by utilizing the ultrafiltration technique and the specific interaction of TiO₂ with the phosphate groups on the lipid bilayer of exosomes. Downstream characterization and proteomic analysis indicate that high-quality exosomes can be obtained from human urine by this ultrafiltration-TiO₂ series method in 20 minutes, and 91.5% exosomes with an intact structure are captured from urine by this method. Moreover, 1874 protein groups have been identified through LC-MS. The results show that the protein identification of our method is 23% higher at least than those obtained by conventional strategies. We also identified 30 differential proteins by comparing the urinary exosomes from healthy male and female volunteers. These proteins are related to biological processes, such as lipid metabolism, fatty acid metabolism and nucleotide metabolism. Our analysis reveals that combining conventional ultrafiltration and TiO₂-based isolation is ideal to overcome the inherent limitations of identification of exosome proteins derived from urine, and yield highly pure exosome components for downstream proteomic analysis.

The gene NtMYC2a acts as a 'master switch' in the regulation of JA-induced nicotine accumulation in tobacco

The biosynthesis and transport of nicotine has been shown to be coordinately upregulated by jasmonate (JA). MYC2, a member of basic helix-loop-helix (bHLH) transcription factor family, is well-documented as the core player in the JA signalling pathway to regulate diverse plant development processes. Four MYC2 genes were found in the tobacco genome, NtMYC2a/2b and 1a/1b. In this study, we tested whether one of them, NtMYC2a, acts as a 'master switch' in the regulation of nicotine biosynthesis and transport in tobacco. We generated NtMYC2a knockout tobacco plants using the CRISPR-Cas9 technique and analysed the effect of NtMYC2a knockout on expression of the nicotine biosynthesis genes (NtAO, NtQS, NtPMT1a, NtQPT2, NtODC2, NtMPO1, NtA622 and NtBBLa) and transport genes (NtMATE2 and NtJAT1), as well as leaf accumulation of nicotine in the NtMYC2a knockout plants. We found that all the nicotine biosynthesis and transport genes tested in this study were significantly downregulated (>50% reduction compared with wild-type control) in the NtMYC2a knockout plants. Moreover, the leaf nicotine content in knockout plants was dramatically reduced by ca 80% compared with the wild-type control. These results clearly show that NtMYC2a acts as a 'master switch' to coordinate JA-induced nicotine accumulation in tobacco and suggests that NtMYC2a might play an important role in tobacco nicotine-mediated defence against herbivory.

A facile "one-material" strategy for tandem enrichment of small extracellular vesicles phosphoproteome

Small extracellular vesicles (SEVs), are cell-derived, membrane-enclosed nanometer-sized vesicles that play vital roles in many biological processes. Recent years, more and more evidences proved that small EVs have close relationship with many diseases such as cancers and Alzheimer's disease. The use of phosphoproteins in SEVs as potential biomarkers is a promising new choice for early diagnosis and prognosis of cancer. However, current techniques for SEVs isolation still facing many challenges, such as highly instrument dependent, time consuming and insufficient purity. Furthermore, complex enrichment procedures and low microgram amounts of proteins available from clinical sources largely limit the throughput and the coveage depth of SEVs phosphoproteome mapping. Here, we synthesized Ti⁴⁺-modified magnetic graphene-oxide composites (GFST) and developed a "one-material" strategy for facile and efficient phosphoproteome enrichment and identification in SEVs from human serum. By taking advantage of chelation and electrostatic interactions between metal ions and phosphate groups, GFST shows excellent performance in both SEVs isolation and phosphopeptide enrichment. Close to 85% recovery is achieved within a few minutes by simple incubation with GFST and magnetic separation. Proteome profiling of the isolated serum SEVs without phosphopeptide enrichment results in 515 proteins, which is approximately one-fold more than those otained by ultracentrifugation or coprecipitation kits. Further application of GFST in one-material-based enrichment led to identification of 859 phosphosites in 530 phosphoproteins. Kinase-substrate correlation analysis reveals enriched substrates of CAMK in serum SEVs phosphoproteome. Therefore, we expect that the low instrument dependency and the limited sample requirement of this new strategy may facilitate clinical investigations in SEV-based transportation of abnormal kinases and substrates for drug target discovery and cancer monitoring.

Novel Two-Dimensional MoS2-Ti4+ Nanomaterial for Efficient Enrichment of Phosphopeptides and Large-Scale Identification of Histidine Phosphorylation by Mass Spectrometry

Due to its key roles in regulating the occurrence and development of cancer, protein histidine phosphorylation has been increasingly recognized as an important form of post-translational modification in recent years. However, large-scale analysis of histidine phosphorylation is much more challenging than that of serine/threonine or tyrosine phosphorylation, mainly because of its acid lability. In this study, MoS₂-Ti⁴⁺ nanomaterials were synthesized using a solvothermal method and taking advantage of the electrostatic adsorption between MoS₂ nanosheets and Ti⁴⁺. The MoS₂-Ti⁴⁺ nanomaterials have the advantage of the combined affinity of Ti⁴⁺ and Mo toward phosphorylation under medium acidic conditions (pH = 3), which is crucial for preventing hydrolysis and loss of histidine phosphorylation during enrichment. The feasibility of using the MoS₂-Ti⁴⁺ nanomaterial for phosphopeptide enrichment was demonstrated using mixtures of β-casein and bovine serum albumin (BSA). Further evaluation revealed that the MoS₂-Ti⁴⁺ nanomaterial is capable of enriching synthetic histidine phosphopeptides from 1000 times excess tryptic-digested HeLa cell lysate. Application of the MoS₂-Ti⁴⁺ nanomaterials for large-scale phosphopeptide enrichment results in the identification of 10 345 serine, threonine, and tyrosine phosphosites and the successful mapping of 159 histidine phosphosites in HeLa cell lysates, therefore indicating great potential for deciphering the vital biological roles of protein (histidine) phosphorylation.

[Advances in separation techniques for exosomes and their clinical applications]

Exosomes are vesicles secreted by many types of cells through exocytosis, and their sizes range from 30 to 200 nm. Exosomes consist of a lipid bilayer membrane, containing a number of bioactive molecules, e. g., proteins, ribose nucleic acid (RNA), and deoxyribo nucleic acid (DNA) derived from the cell of origin. As intercellular communication carriers, exosomes participate in many physiological and pathological processes. Because of the complexity of body fluids, as well as the small size and low density of exosomes, the isolation of exosomes is an essential and challenging step before subsequent analysis and functional studies. This review summarizes the advances in the analytical approaches, characterization methods, biological functions and clinical applications of exosomes, with particular emphasis on exosomes isolation techniques.

Operating behavior of micro-LEDs on a GaN substrate at ultrahigh injection current densities

Near-ultraviolet micro-LEDs with different diameters were fabricated on GaN substrates. The electroluminescence and the light output power-current density and current density-voltage relationships were measured. A saturated current density of 358 kA/cm² was achieved with a 20 µm LED. The ideality factor curves showed steps and peaks when the injection current density was increased from 20 to 150 kA/cm² and an abnormal efficiency increase. The transport and recombination processes of micro-LEDs at high injection current densities were simulated, and the many-body effect and phase space filling in the integrated quantum drift-diffusion model were considered. Serious current crowding was observed above 100 kA/cm², even for the 20 µm LED.

A novel strategy for facile serum exosome isolation based on specific interactions between phospholipid bilayers and TiO2

Exosomes are cell-derived, phospholipid bilayer-enclosed vesicles that play important roles in intercellular interactions and regulate many biological processes. Accumulating evidence suggests that serum exosomes are potential biomarkers for the early diagnosis of cancer. To aid the downstream molecular analyses of tumour-secreted exosomes, purified exosomes are highly desirable. However, current techniques for exosome isolation are time-consuming and highly instrument-dependent, with limited specificity and recovery. Thus, rapid and efficient methods are strongly needed for both basic research and clinical applications. Here, we present a novel strategy for facile exosome isolation from human serum by taking advantage of the specific interaction of TiO2 with the phosphate groups on the lipid bilayer of exosomes. Due to their simplicity and highly affinitive binding, model exosomes can be reversibly isolated with a high recovery (93.4%). Downstream characterization and proteome profiling reveal that high-quality exosomes can be obtained from human serum by this TiO2-based isolation method in 5 min, which is a fraction of the time required for the commonly used ultracentrifugation method. We identified 59 significantly up-regulated proteins by comparing the serum exosomes of pancreatic cancer patients and healthy donors. In addition to the 30 proteins that were reported to be closely related to pancreatic cancer, we found an additional 29 proteins that had not previously been shown to be related to pancreatic cancer, indicating the potential of this novel method as a powerful tool for exosome isolation for health monitoring and disease diagnosis.

Two-Dimensional MoS2-Based Zwitterionic Hydrophilic Interaction Liquid Chromatography Material for the Specific Enrichment of Glycopeptides

Mass spectrometry (MS)-based glycoproteomics research requires highly efficient sample preparation to eliminate interference from non-glycopeptides and to improve the efficiency of glycopeptide detection. In this work, a novel MoS₂/Au-NP (gold nanoparticle)-L-cysteine nanocomposite was prepared for glycopeptide enrichment. The two-dimensional (2D) structured MoS₂ nanosheets served as a matrix that could provide a large surface area for immobilizing hydrophilic groups (such as L-cysteine) with low steric hindrance between the materials and the glycopeptides. As a result, the novel nanomaterial possessed an excellent ability to capture glycopeptides. Compared to commercial zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) materials, the novel nanomaterials exhibited excellent enrichment performance with ultrahigh selectivity and sensitivity (approximately 10 fmol), high binding capacity (120 mg g^-1), high enrichment recovery (more than 93%), satisfying batch-to-batch reproducibility, and good universality for glycopeptide enrichment. In addition, its outstanding specificity and efficiency for glycopeptide enrichment was confirmed by the detection of glycopeptides from an human serum immunoglobulin G (IgG) tryptic digest in quantities as low as a 1:1250 molar ratio of IgG tryptic digest to bovine serum albumin tryptic digest. The novel nanocomposites were further used for the analysis of complex samples, and 1920 glycopeptide backbones from 775 glycoproteins were identified in three replicate analyses of 50 μg of proteins extracted from HeLa cell exosomes. The resulting highly informative mass spectra indicated that this multifunctional nanomaterial-based enrichment method could be used as a promising tool for the in-depth and comprehensive characterization of glycoproteomes in MS-based glycoproteomics.

Detection of porcine circovirus-like virus P1 in Hebei, China

Porcine circovirus-like virus P1 is a novel unclassified circovirus that was first detected in China and may be associated with post-weaning multisystemic wasting syndrome (PMWS) and congenital tremor. In this study, we detected P1 infection in pigs in Hebei Province, China, in 2017. One hundred and forty of 500 (28.0%) serum samples from 25 pig farms with different PMWS status in seven cities were P1 positive on PCR. Twelve P1 strains were sequenced, and the complete genomes of 11 P1 strains were 648 nucleotides (nt) in length, whereas that of strain ZJK02 was 647 nt, with a G deletion at position of 183 in its genome. The complete genomic and capsid protein sequences of the 12 P1 strains analysed in this study shared 98.8%-100.0% and 86.5%-100.0% identity, respectively. A phylogenetic analysis based on the complete genomic and capsid sequences of 26 P1 strains showed that the 12 P1 sequences from Hebei Province clustered on two small branches. Further studies of the evolution and pathogenesis of P1 are required.

Long Non-Coding RNA: An Emerging Paradigm of Pancreatic Cancer

Pancreatic cancer remains a worldwide issue and burden that is hard to resolve given its low resection rate and chemo-resistance. Early diagnosis and early treatment are critical for conquering pancreatic cancer. Therefore, new biomarkers for diagnosis and prognosis are urgently needed. Previously, researchers mainly focused on protein-coding genetic and epigenetic changes in many types of cancers, and regarded the noncoding part as waste. Recently, however, long non-coding RNA (lncRNA) has emerged as a major participant in carcinogenesis, as it regulates cell proliferation, migration, invasion, metastasis, chemo-resistance, etc. The underlying mechanisms are summarized as signaling, decoy, guide and scaffold, yet the specific regulation networks remain to be uncovered. Several studies have revealed that some lncRNAs are dysregulated in pancreatic cancer, participating in biological functions. In this review, we will briefly outline the functional lncRNAs in pancreatic cancer, decipher possible mechanisms of lncRNAs, and further explore their significance in pancreatic cancer.

Annual direct medical costs associated with diabetes-related complications in the event year and in subsequent years in Hong Kong

AIM

To develop models to estimate the direct medical costs associated with diabetes-related complications in the event year and in subsequent years.

METHODS

The public direct medical costs associated with 13 diabetes-related complications were estimated among a cohort of 128 353 people with diabetes over 5 years. Private direct medical costs were estimated from a cross-sectional survey among 1825 people with diabetes. We used panel data regression with fixed effects to investigate the impact of each complication on direct medical costs in the event year and subsequent years, adjusting for age and co-existing complications.

RESULTS

The expected annual public direct medical cost for the baseline case was US$1,521 (95% CI 1,518 to 1,525) or a 65-year-old person with diabetes without complications. A new lower limb ulcer was associated with the biggest increase, with a multiplier of 9.38 (95% CI 8.49 to 10.37). New end-stage renal disease and stroke increased the annual medical cost by 5.23 (95% CI 4.70 to 5.82) and 5.94 (95% CI 5.79 to 6.10) times, respectively. History of acute myocardial infarction, congestive heart failure, stroke, end-stage renal disease and lower limb ulcer increased the cost by 2-3 times. The expected annual private direct medical cost of the baseline case was US$187 (95% CI 135 to 258) for a 65-year-old man without complications. Heart disease, stroke, sight-threatening diabetic retinopathy and end-stage renal disease increased the private medical costs by 1.5 to 2.5 times.

CONCLUSIONS

Wide variations in direct medical cost in event year and subsequent years across different major complications were observed. Input of these data would be essential for economic evaluations of diabetes management programmes.

Polymeric hydrophilic ionic liquids used to modify magnetic nanoparticles for the highly selective enrichment of N-linked glycopeptides

The low abundance of glycopeptides in biological samples makes it necessary to enrich them before further analysis. In this study, the polymeric hydrophilic ionic liquid-modified magnetic (Fe₃O₄@MPS@PMAC) nanoparticles were synthesized via a one-step reflux-precipitation polymerization. Owing to the excellent hydrophilicity and strong electrostatic interaction toward glycopeptides of the polymerized hydrophilic ionic liquid, [2-(methacryloyloxy) ethyl] trimethylammonium chloride (MAC), the synthesized Fe₃O₄@MPS@PMAC nanoparticles exhibited outstanding performance in glycopeptide enrichment with high detection sensitivity (10 fmol), large binding capacity (100 μg mg^-1) and satisfied enrichment recovery (approximately 82%). Furthermore, the newly developed Fe₃O₄@MPS@PMAC nanoparticles were applied for the glycopeptide enrichment of HeLa exosome proteins. A total of 1274 glycopeptides from 536 glycoproteins were identified in three replicate analyses of 50 μg of HeLa exosome proteins. These results demonstrate the potential of Fe₃O₄@MPS@PMAC nanoparticles for both glycoproteomic analysis and exosome research.

Experimental and observational studies find contrasting responses of soil nutrients to climate change

Manipulative experiments and observations along environmental gradients, the two most common approaches to evaluate the impacts of climate change on nutrient cycling, are generally assumed to produce similar results, but this assumption has rarely been tested. We did so by conducting a meta-analysis and found that soil nutrients responded differentially to drivers of climate change depending on the approach considered. Soil carbon, nitrogen, and phosphorus concentrations generally decreased with water addition in manipulative experiments but increased with annual precipitation along environmental gradients. Different patterns were also observed between warming experiments and temperature gradients. Our findings provide evidence of inconsistent results and suggest that manipulative experiments may be better predictors of the causal impacts of short-term (months to years) climate change on soil nutrients but environmental gradients may provide better information for long-term correlations (centuries to millennia) between these nutrients and climatic features. Ecosystem models should consequently incorporate both experimental and observational data to properly assess the impacts of climate change on nutrient cycling.

DOI:http://dx.doi.org/10.7554/eLife.23255.001

Facile synthesis of magnetic covalent organic frameworks for the hydrophilic enrichment of N-glycopeptides

Magnetic covalent organic frameworks were synthesized as novel hydrophilic materials for specific enrichment of glycopeptides.

Development and application of immobilized surfactant in mass spectrometry-based proteomics

The synthesis process of Fe₃O₄@TMOS, a surfactant for the pretreatment of complex biological samples.

Metal ion-immobilized magnetic nanoparticles for global enrichment and identification of phosphopeptides by mass spectrometry

Highly selective and sensitive enrichment for global phosphopeptides by novel magnetic nanoparticles Fe₃O₄@TCPP-DOTA-Ms.

A novel microscale preparative gel electrophoresis system

A novel microscale preparative gel electrophoresis system is designed and manufactured for protein separation and preparation.

Hollow silica bubble based immobilized trypsin for highly efficient proteome digestion and buoyant separation

Tryptic digestion before identification and quantification by mass spectrometry is an indispensable process for most proteomics studies.

Association between single-nucleotide polymorphisms of fatty acid synthase gene and meat quality traits in Datong Yak (Bos grunniens)

Fatty acid synthase (FASN) is a key enzyme in fatty acid anabolism that plays an important role in the fat deposit of eukaryotic cells. Therefore, in this study, we detected 2 novel single-nucleotide polymorphisms (SNPs) in the FASN gene in 313 adult individuals of Datong yak using polymerase chain reaction-single strand conformation polymorphism and DNA sequencing techniques. SNP g.5477C>T is located in intron 3 of FASN, and 3 genotypes, HH, HG, and GG, were detected in this mutation site. SNP g.16930T>A is located in exon 37 of FASN, and 2 genotypes, EE and EF, were detected in this site. Association analysis of these 2 SNPs with meat quality traits showed that in SNP g.5477C>T, yaks with the HH genotype and HG genotype had significantly higher intramuscular fat content than individuals with the GG genotype (P < 0.01). In SNP g.16930T>A, yaks with the EE genotype also had significantly higher IMF content than individuals with the EF genotype (P < 0.01). The results indicate that FASN may be used as a candidate gene affecting intramuscular fat content in Datong yaks.

A new sample preparation method for the absolute quantitation of a target proteome using 18O labeling combined with multiple reaction monitoring mass spectrometry

A new sample preparation method for target proteome absolute quantitation using ¹⁸O labeling-MRM MS.

[Progress in metal-organic frameworks]

Metal-organic frameworks (MOFs) are a class of crystalline materials built from organic binding ligands and metal ions through self-assembly. Currently, MOFs have drawn a growing interest among the scientific teams of various fields. Compared with conventional inorganic porous materials, MOFs possess larger specific surface areas, higher porosity and diversity of structures and functions, thus many potential applications have been proposed in the domains of gas adsorption and separation, sensors, drug delivery, catalysis or others. The combinations of MOFs and other materials such as graphene oxide, magnetic nanoparticles have obvious advantages in adsorption and separation. The appearance of novel materials greatly promotes interdisciplinary developments such as organic chemistry, inorganic chemistry, coordination chemistry, materials chemistry, life science and computer science. This article reviews the progress of MOFs in recent years, including the characteristics of MOFs, advances at home and abroad, applications, central issues of compound MOFs and the prospects in the future.

Microfluidic laminate-based phantom for diffusion tensor-magnetic resonance imaging (DT-MRI)

This paper reports fabrication of a magnetic resonance imaging (MRI) phantom created by stacking of multiple thin polydimethylsiloxane (PDMS) layers. PDMS is spin coated on SU-8 molds to obtain the desired layer thickness and imprints of the microchannel patterns that define the phantom geometry. This paper also identifies the unique challenges related to the fabrication and assembly of multiple thin layers and reports for the first time assembly of a large number of thin laminates of this nature. Use of photolithography techniques allows us to create a wide range of phantom geometries. The target dimensions of the phantoms reported here are (i) a stack of 30 thin PDMS layers of 10 µm thickness (ii) curved 5 µm × 5 µm microchannels with 8.7 µm spacing, and (iii) straight 5 µm × 5 µm microchannels with 3.6 µm spacing. SEM scans of the assembled phantoms show open microchannels and a monolithic cross-section with no visible interface between PDMS layers. Based on the results of diffusion tensor magnetic resonance imaging (DT-MRI) scan, the anisotropic diffusion of water molecules due to the physical restriction of the microchannels was detected, which means that the phantom can be used to calibrate and optimize MRI instrumentation.

Involvement of the mitochondrial pathway in p53-independent apoptosis induced by p28GANK knockdown in Hep3B cells

It is well known that TP53 may mediate apoptosis triggered by anticancer drugs. However, accumulating evidence indicates that TP53 may be inactivated by mutations and/or deletions in about 50% of human cancers and, as such, may lead to pronounced resistance to therapeutic agents. Thus, the development of new approaches to improve the efficiency of therapeutic agents in cancer cells harboring mutant TP53 may have a significant impact on cancer treatment. It has been reported that knockdown by RNA interference (RNAi) of p28GANK (an alias of the gene PSMD10), a novel oncogene over-expressed in hepatocellular carcinoma (HCC), can induce apoptosis in HepG2, a TP53-intact HCC cell line. Because of the high frequency TP53 mutations in HCC, it is relevant to know whether p28GANK knockdown-induced apoptosis is also operational in TP53-negative HCC cells. Here, we investigated Adsip28GANK-induced apoptosis in the TP53-negative HCC cell line Hep3B. Our results indicate that p28GANK-knockdown induces the generation of reactive oxygen species (ROS), which in turn activates p38. Since p38 can signal to Bax, its activation may lead to mitochondrial transmembrane potential (Delta psi m) loss, cytochrome c release from mitochondria to cytosol, and caspase-9 activation, eventually triggering the mitochondrial pathway of apoptosis.

[Inhibiting gene expression in vivo by virus-mediated small interfering RNA]

Inhibiting gene expression in specific tissues and organs through intravenous injection would be the ultimately preferred method of disease therapy. Here, we report the successful delivery of lentivirus-mediated small interfering RNA (siRNA) to suppress the GFP gene expression in living mice. First, a lentiviral vector with siRNA (len-siRNA) driven by H1 promoter was constructed to suppress GFP expression effectively in Mel cells. When the len-siRNA virus was injected into transgenic mice, the GFP expression was significantly suppressed (over 15% reduction) in the recipient mice compared to the control mice and the suppressing effect lasted more than one week after injection. Our results demonstrate a new effective approach to inhibit gene expression by siRNA and lentiviral vectors. Further development of this suppression of gene expression siRNA drug should result in applications not only for cancers but also for infectious and immune diseases.

[Establishment and application of a two-dimensional liquid chromatographic system (NPLC x RPLC)]

A two-dimensional liquid chromatographic system (NPLC x RPLC) has been developed. Normal phase liquid chromatography (NPLC) with a Hypersil SiO2 column (50 mm x 4.6 mm) was used as the first dimension, and reversed-phase liquid chromatography (RPLC) with a Kromasil C18 column (250 mm x 4.6 mm) was used as the second dimension. The interface was a ten-port, two-position valve with two storage loops. As to improve the compatibility of the two dimensional mobile phase and be good for adjusting the selectivity of separation, 1,4-dioxane was used in the mobile phase of the first dimension, and isopropyl alcohol was used in the mobile phase of the second dimension based on the characters of the organic solvents. By raising the temperature of the second dimension, the incompatibility of the two dimensional mobile phases was avoided. A Chinese potent medicine, Zhengtian Wan, was analyzed by this system. The total peak capacity reached 1 220.

[Substitution of diphenyl sulfurine to trinuclear clusters and infrared spectra characterization]

Substitution of diphenyl sulfurine to dodecarbonyl-triruthenium and dodecarbonyl-triiron were studied respectively. Infrared spectra were used in characterization of the reactions and to follow the reaction processes from starting to finishing. Spectra data showed that the new compounds appeared and starting materials disappeared. The results products Ru3 (CO)9CSN2HPh2 and Fe3 (CO)8S2CNPh were taken in KBr pellet infrared spectras. C, S and N in diphenyl sulfurine might coordinate to transitionmetal atoms in the clusters. Since trinuclear ruthenium and iron clusters have different stability and diphenyl sulfurine induced attacked to cluster skeleton in reaction, Ru3 (CO)12 and Fe3 (CO)12 give different coordination structure trinuclear Ru and Fe clusters, in which every metal atom forms 18 e constitution.

[Study in coordination substitution of trinuclear iron and ruthenium clusters by infrared and ultraviolet spectroscopy]

In this paper, ultraviolet spectra and infrared spectra were used in the characterization of the reaction in which carbonyls in trinuclear-iron cluster and trinuclear-ruthenium cluster were substituted by Ph2C2 and PPh3 respectively. The spectra showed the process of the new compounds appear and starting materials disappear separately. Infrared spectra data in KBr pellets further proved the result products. Reaction of Ru3(CO)12 with PPh3 (mol ratio = 1:3) in hexane affords Ru3(CO)9 (PPh3)3, a red microcrystalline solid and Fe3(CO)12 with Ph2C2 (mol ratio = 1:1) affords Fe3(CO)10 (Ph2C2) a deep green crystals. In the study, the ultraviolet spectra and infrared spectra of reaction solutions changed following the reactions, given a information in which we known the reaction starting and finishing. Then new compounds possibly were separated from reaction solutions. This is an important method used for synthesis and catalysis.

Epidemiologic and clinical characteristics of Kawasaki disease in Shaanxi Province, China, 1993-1997

The objective of this paper is to describe the epidemiological and clinical characteristics of Kawasaki disease (KD) in Shaanxi Province, China during the 5-year period from January 1993 to December 1997. A province-wide epidemiological survey on KD was made by the China-Japan Kawasaki Disease Study Group. The questionnaire form and the diagnostic criteria of KD, which were prepared by the Japan Kawasaki Disease Research Committee and translated into Chinese, were sent to the departments of pediatrics of all the hospitals with 100 beds or more in Shaanxi province. All the KD patients who were diagnosed during the observation period from 1993 to 1997 were asked to take part in this survey. The databases of reported KD in this survey were analysed at the Department of Pediatrics of the Shaanxi Provincial People's Hospital, Xi'an, China. All the patients that satisfied the diagnostic criteria were included in the report. A total of 105 (70 per cent) hospitals responded and 376 cases of KD were confirmed. More cases were reported in 1993 and 1994. Of the total patients reported, 69 per cent were children under 3 years old with a male to female ratio of 1.6:1. The proportion of patients with cardiac sequelae was 19 per cent with a male to female ratio of 3:1. There were four fatal cases with a fatality rate of 1 per cent. It is concluded that KD is common in China. Continuous surveillance is necessary to maintain high awareness of KD so as to find possible risk factors and their association with the disease.

[A clinical and epidemiological study of 86 cases on abused children]

OBJECTIVE

To study the clinical and epidemiological manifestations on abused children, in order to find ways of prevention.

METHODS

Retrospective study was carried out clinically and epidemiologically on 86 cases abused children from 1998.1 - 1999.12.

RESULTS

The sex ratio (male:female) in the abused children was 0.76:1. Most cases were 3 - 16 years olds. Abuse incidences were most commonly occurred in spring and winter, accounted for 32.56% and 33.72% respectively. Most abuses happened physically (45.34%), predominantly involved skin (30.23%) and parenchyma (11.27%). Mental abuse accounted for 24.41%. 14 cases resulted in death (16.27%). 55 (64%) of the abusers were illiterate or with poor education.

CONCLUSION

The abused sites mostly involved skin and parenchyma, but also caused harm to children's mental health, even causing deaths. Most abused children were female and abusers had lower cultural background. Thus, we need to provide a sounding board, to work on child abuse preventin.

[Epidemiological and clinical characteristics of Kawasaki disease in Shanxi province]

OBJECTIVE

The objective of this paper is to describe the epidemiological and clinical characteristics of Kawasaki disease (KD) in Shanxi province, China during a 5 year - period from January 1993 to December 1997.

METHODS

A province - wide epidemiological survey on Kawasaki disease (KD) was carried ont by the China - Japan Kawasaki disease study group. The questionnaire form and the diagnostic criteria of KD which was prepared by the Japan Kawasaki disease research committee and translated into Chinese were sent of the departments of pediatrics of all the hospitals with 100 or more beds in Shanxi province. All the KD patients who were diagnosed during the observation period from 1993 to 1997 were asked to report to this survey. The database of reported KD in this survey was analyzed at the Department of pediatrics of the Shanxi provincial people's hospital, Xian, China. All the patients that satisfied the diagnostic criteria were included.

RESULTS

A total of 105 (70%) hospitals responded and 376 cases of KD were confirmed. More cases were reported in 1993 and 1994. Of the total patients reported, 69% were children under 3 years old with male to female ratio of 1.6:1. The proportion of patients with cardiac sequelae was 19% with male to female ratio: 3:1. There were 4 fatal cases with a fatality rate of 1%.

CONCLUSIONS

Since KD is common in China continuous surveillance is necessary to maintain high awareness of KD so as to identify possible risk factors and its association with other disease.