An Improvement of Shotgun Proteomics Analysis by Adding Next-Generation Sequencing Transcriptome Data in Orange

BACKGROUND: Shotgun proteomics data analysis usually relies on database search. Because commonly employed protein sequence databases of most species do not contain sufficient protein information, the application of shotgun proteomics to the research of protein sequence profile remains a big challenge, especially to the species whose genome has not been sequenced yet. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, we present a workflow with integrated database to partly address this problem. First, we downloaded the homologous species database. Next, we identified the transcriptome of the sample, created a protein sequence database based on the transcriptome data, and integtrated it with homologous species database. Lastly, we developed a workflow for identifying peptides simultaneously from shotgun proteomics data. CONCLUSIONS/SIGNIFICANCE: We used datasets from orange leaves samples to demonstrate our workflow. The results showed that the integrated database had great advantage on orange shotgun proteomics data analysis compared to the homologous species database, an 18.5% increase in number of proteins identification

Time to full enteral feeding for very low-birth-weight infants varies markedly among hospitals worldwide but may not be associated with incidence of necrotizing enterocolitis:The NEOMUNE-NeoNutriNet Cohort Study

Background: Transition to enteral feeding is difficult for very low-birth-weight (VLBW; ≤1500 g) infants, and optimal nutrition is important for clinical outcomes. Method: Data on feeding practices and short-term clinical outcomes (growth, necrotizing enterocolitis [NEC], mortality) in VLBW infants were collected from 13 neonatal intensive care units (NICUs) in 5 continents (n = 2947). Specifically, 5 NICUs in Guangdong province in China (GD), mainly using formula feeding and slow feeding advancement (n = 1366), were compared with the remaining NICUs (non-GD, n = 1581, Oceania, Europe, United States, Taiwan, Africa) using mainly human milk with faster advancement rates. Results: Across NICUs, large differences were observed for time to reach full enteral feeding (TFF; 8–33 days), weight gain (5.0–14.6 g/kg/day), ∆z-scores (−0.54 to −1.64), incidence of NEC (1%–13%), and mortality (1%–18%). Adjusted for gestational age, GD units had longer TFF (26 vs 11 days), lower weight gain (8.7 vs 10.9 g/kg/day), and more days on antibiotics (17 vs 11 days; all P <.001) than non-GD units, but NEC incidence and mortality were similar. Conclusion: Feeding practices for VLBW infants vary markedly around the world. Use of formula and long TFF in South China was associated with more use of antibiotics and slower weight gain, but apparently not with more NEC or higher mortality. Both infant- and hospital-related factors influence feeding practices for preterm infants. Multicenter, randomized controlled trials are required to identify the optimal feeding strategy during the first weeks of life

Genetic Variants at 1p11.2 and Breast Cancer Risk: A Two-Stage Study in Chinese Women

BACKGROUND: Genome-wide association studies (GWAS) have identified several breast cancer susceptibility loci, and one genetic variant, rs11249433, at 1p11.2 was reported to be associated with breast cancer in European populations. To explore the genetic variants in this region associated with breast cancer in Chinese women, we conducted a two-stage fine-mapping study with a total of 1792 breast cancer cases and 1867 controls. METHODOLOGY/PRINCIPAL FINDINGS: Seven single nucleotide polymorphisms (SNPs) including rs11249433 in a 277 kb region at 1p11.2 were selected and genotyping was performed by using TaqMan® OpenArray™ Genotyping System for stage 1 samples (878 cases and 900 controls). In stage 2 (914 cases and 967 controls), three SNPs (rs2580520, rs4844616 and rs11249433) were further selected and genotyped for validation. The results showed that one SNP (rs2580520) located at a predicted enhancer region of SRGAP2 was consistently associated with a significantly increased risk of breast cancer in a recessive genetic model [Odds Ratio (OR)  =  1.66, 95% confidence interval (CI)  =  1.16-2.36 for stage 2 samples; OR  =  1.51, 95% CI  =  1.16-1.97 for combined samples, respectively]. However, no significant association was observed between rs11249433 and breast cancer risk in this Chinese population (dominant genetic model in combined samples: OR  =  1.20, 95% CI  =  0.92-1.57). CONCLUSIONS/SIGNIFICANCE: Genotypes of rs2580520 at 1p11.2 suggest that Chinese women may have different breast cancer susceptibility loci, which may contribute to the development of breast cancer in this population

Electrically Guiding Migration of Human Induced Pluripotent Stem Cells

A major road-block in stem cell therapy is the poor homing and integration of transplanted stem cells with the targeted host tissue. Human induced pluripotent stem (hiPS) cells are considered an excellent alternative to embryonic stem (ES) cells and we tested the feasibility of using small, physiological electric fields (EFs) to guide hiPS cells to their target. Applied EFs stimulated and guided migration of cultured hiPS cells toward the anode, with a stimulation threshold of <30 mV/mm; in three-dimensional (3D) culture hiPS cells remained stationary, whereas in an applied EF they migrated directionally. This is of significance as the therapeutic use of hiPS cells occurs in a 3D environment. EF exposure did not alter expression of the pluripotency markers SSEA-4 and Oct-4 in hiPS cells. We compared EF-directed migration (galvanotaxis) of hiPS cells and hES cells and found that hiPS cells showed greater sensitivity and directedness than those of hES cells in an EF, while hES cells migrated toward cathode. Rho-kinase (ROCK) inhibition, a method to aid expansion and survival of stem cells, significantly increased the motility, but reduced directionality of iPS cells in an EF by 70–80%. Thus, our study has revealed that physiological EF is an effective guidance cue for the migration of hiPS cells in either 2D or 3D environments and that will occur in a ROCK-dependent manner. Our current finding may lead to techniques for applying EFs in vivo to guide migration of transplanted stem cells

A novel porous Ti6Al4V: characterization and cell attachment

For the first time, a highly porous strong Ti6Al4V was produced by using a polymeric sponge replication method. A polymeric sponge, impregnated with a Ti6Al4V slurry prepared from Ti6Al4V powders and binders, was subjected to drying and pyrolyzing to remove the polymeric sponge and binders. After sintering at a high temperature and under high vacuum, a porous Ti6Al4V was produced. Optical microscopical observation, environmental scanning electron microscopy observation (with energy-dispersive micro X-ray analysis), mechanical tests, and metallurgical analyses were performed on the obtained porous Ti6Al4V with regard to the porous structure (both macropores and micropores), mechanical properties, chemical composition, phase compositions, and cell attachment behavior. The porous Ti6Al4V made by this method had a three-dimensional trabecular porous structure with interconnected pores mainly ranging from 400 to 700 m and a total porosity of about 90%. The compressive strength was 10.3 ± 3.3 MPa and the elastic constant 0.8 ± 0.3 GPa. MC3T3-E1 cells attached and spread well in the inner surface of pores. Being similar to cancellous bone with regard to both interconnected porous structure and mechanical properties, the resulting porous Ti6Al4V is expected to be a promising biomaterial for biomedical applications

Macroporous biphasic calcium phosphate scaffold with high permeability/porosity ratio

Macroporous biphasic calcium phosphate (BCP) with channel-shaped pores was produced by a novel dual-phase mixing method. The processing route includes mixing water-based BCP slurry and polymethylmethacrylate resin; shaping in a mold; and polymerization, drying, pyrolyzing, and sintering. After comparison with two other commercial macroporous BCP materials, which were produced along different routes, it was found that conventional parameters such as porosity and pore size cannot describe a macroporous structure precisely enough for the application as tissue-engineering scaffold. Instead, permeability can be seen as an intrinsic and quantitative parameter to describe the macroporous structure of various scaffolds, because it is independent of sample size and fluid used in the test. Another parameter, the permeability/porosity ratio, provides an indication of the percolative efficiency per unit porous volume of a scaffold. Structural characterizations and permeability studies of other macroporous scaffold materials were also performed, and it was found that permeability could reflect a combination of five important parameters for scaffold: (1) porosity, (2) pore size and distribution, (3) interconnectivity, (4) fenestration size and distribution, and (5) orientation of pores. Finally, the implications of relating permeability with biological performances are also discussed

The effect of scaffold architecture on properties of direct 3D fiber deposition of porous Ti6Al4V for orthopedic implants

3D porous Ti6Al4V scaffolds were directly fabricated by a rapid prototyping technology, 3D fiber deposition (3DF). In this study, scaffolds with different structures were fabricated by changing fiber spacing and fiber orientation. The influence of different architectures on mechanical properties and permeability of the scaffold were investigated. Mechanical analysis revealed that compressive strength and E-modulus increase with decreasing the porosity. Permeability measurements showed that not only the total porosity but also the porous structure can influence the permeability. 3DF was found to provide good control and reproducibility of the desired degree of porosity and the 3D structure. Results of this study demonstrate that the 3DF of Ti6Al4V give us flexibility and versatility to fabricate and improve scaffolds to better mimic the architecture and properties of natural bone and meet the requirements of bone graft substitutes and orthopedic and dental implants

Porous Ti6Al4V scaffold directly fabricating by rapid prototyping: preparation and in vitro experiment

Three-dimensional (3D) fiber deposition (3DF), a rapid prototyping technology, was successfully directly applied to produce novel 3D porous Ti6Al4V scaffolds with fully interconnected porous networks and highly controllable porosity and pore size. A key feature of this technology is the 3D computer-controlled fiber depositing of Ti6Al4V slurry at room temperature to produce a scaffold, consisting of layers of directionally aligned Ti6Al4V fibers. In this study, the Ti6Al4V slurry was developed for the 3D fiber depositing process, and the parameters of 3D fiber depositing were optimized. The experimental results show how the parameters influence the structure of porous scaffold. The potential of this rapid prototyping 3DF system for fabricating 3D Ti6Al4V scaffolds with regular and reproducible architecture meeting the requirements of tissue engineering and orthopedic implants is demonstrated