Prediction of Protein Expression and Growth Rates by Supervised Machine Learning

The DNA sequences of an organism play an important influence on its transcription and translation process, thus affecting its protein production and growth rate. Due to the com-plexity of DNA, it was extremely difficult to predict the macroscopic characteristics of or-ganisms. However, with the rapid development of machine learning in recent years, it be-comes possible to use powerful machine learning algorithms to process and analyze biolog-ical data. Based on the synthetic DNA sequences of a specific microbe, E. coli, I designed a process to predict its protein production and growth rate. By observing the properties of a data set constructed by previous work, I chose to use supervised learning regressors with encoded DNA sequences as input features to perform the predictions. After comparing different encoders and algorithms, I selected three encoders to encode the DNA sequences as inputs and trained seven different regressors to predict the outputs. The hy-per-parameters are optimized for three regressors which have the best potential prediction performance. Finally, I successfully predicted the protein production and growth rates, with the best R2 score 0.55 and 0.77, respectively, by using encoders to catch the potential fea-tures from the DNA sequences.

ANTIBODY TO ONCOGENE PROTEIN PRODUCT AND ITS CONJUGATE WITH RICIN A-CHAIN

The proteins encoded by oncogene were thought to be tumor associated antigen. The protein P110 in MGC803, a human gastric cancer cell line, was purified as immunogen. The IgY to the gastric cancer was extracted from eggs laid by immunized hen. The IgY could react immunohistochemically with gastric cancers. Positive staining rates of PAF were 80% in gastric cancers and markedly higher than in cancers of other organs and normal gastric tissue. The IgY-Ricin A was synthesized by the IgY conjugated with Ricin A- chain. TCID50 of MGC803 treated by the IgY-Ricin A was 0. 01 mg/ml and markedly lower than other cell. These results showed the IgY-Ricin A were able to react with gastric cancers selectively.

Macronutrient Composition and Digestibility of Extruded and Fermented Soya Protein Products

The macronutrient composition and in vitro protein digestibility of extruded fermented and unfermented extruded soya protein products （low, medium and high moisture）, raw and fermented soya meal and soya kernel were studied. The protein content （g/100g soya dry weight） ranged from 38.20 to 62.98 with the highest content in the high moisture extruded protein product fermented with 5 mL inoculum of Bacillus natto. Contents of carbohydrates ranged from 14.77 to 29.08 while those of crude fibre, fat and ash were generally low. Fermentation better improved protein digestibility in the raw soya meal and kernel than in the unfermented extruded and extruded fermented products. SDS-PAGE electrophoresis revealed some degradation of the protein sub units of fermented samples.

New development of whey protein products as nutritional food ingredients

Whey protein products provided ideal ingredients for nutritional food applications.Whey proteins are known to have high nutritional quality due to their high content of essential amino acids,high digestibility and biological value.Research in the past decades has shown that many of the whey protein fractions and peptides derived from them possess various biological activities.The technology developments in the last decade,such as those in the areas of protein fractionation technologies have made industrial scale production of fractionated whey protein products commercially feasible.The development in hydrolysis technology and the peptide analytical capability allowed production of whey protein hydrolysates with designed bioactivity and functionalities.People are continuously finding new biological activities of the various whey protein fractions or their hydrolysis products.Significant amount of research has also been carried out to study the clinical benefits of some of the whey protein fractions and whey protein derived peptides.Examples of these studies will be reviewed and discussed.

Nutralys pea protein Sustainable and innovative product from Roquette

What is sustainable development and what should we do?First definition of sustainable development given in 1987 by world Commission on Environment and Development (Bruntland Commission),it is the most often-quoted definition:

p53 antibodies,metallothioneins,and oxidative stress markers in chronic ulcerative colitis with dysplasia

AIM:To investigate the role of p53 antibodies (p53Abs),metallothioneins (MTs) and oxidative stress markers in the early detection of dysplasia in chronic ulcerative colitis (UC).METHODS:The study included 30 UC patients,15 without dysplasia (group Ⅱ) and 15 with dysplasia (group Ⅲ),in addition to 15 healthy volunteers (group Ⅰ,control subjects).The enzyme-linked immunosorbent assay technique was used to measure serum p53Abs and MTs,while advanced oxidation protein products (AOPPs),and reduced glutathione (GSH) levels were measured by spectrophotometric method in all subjects.RESULTS:In group Ⅱ and group Ⅲ compared to group Ⅰ,there were significant increases in serum levels of AOPPs (145.94 ± 29.86 μmol/L and 192.21 ± 46.71 μmol/L vs 128.95 ± 3.06 μmol/L,P < 0.002 and P <0.001,respectively),MTs (8.18 ± 0.35 μg/mL and 9.20 ± 0.58 μg/mL vs 6.12 ± 0.25 μg/mL,P < 0.05 and P < 0.05,respectively),and p53Abs (20.19 ± 3.20 U/mL and 34.66 ± 1.34 U/mL vs 9.42 ± 1.64 U/mL,P < 0.001 and P < 0.001,respectively).There were significantly higher levels of AOPPs (P < 0.05) and p53Abs (P < 0.001) in UC patients with dysplasia compared to those without dysplasia,while MTs showed no significant difference between the 2 groups (P > 0.096).In contrast,GSH levels showed a significant decrease in both patients' groups (1.87 ± 0.02 μmol/mL and 1.37 ± 0.09 μmol/mL vs 2.49 ± 0.10 μmol/mL,P < 0.05 and P < 0.05 in groups Ⅱ and Ⅲ,respectively) compared with group Ⅰ,and the levels were significantly lower in group Ⅲ than group Ⅱ (P < 0.05).There was a positive correlation between AOPPs and both MTs (r=0.678,P < 0.001) and p53Abs (r=0.547,P < 0.001),and also between p53Abs and MTs (r=0.739,P < 0.001).There was a negative correlation between AOPPs and GSH (r =-0.385,P < 0.001),and also between GSH and both MTs (r=-0.662,P < 0.001) and p53Abs (r=-0.923,P < 0.001).CONCLUSION:Oxidative stress and oxidative cellular damage play an important role in the pathogenesis of chronic UC and the associated carcinogenetic process.p53Abs levels could help in early detection of dysplasia in these conditions.

Beta-nerve growth factor promotes neurogenesis and angiogenesis during the repair of bone defects

We previously showed that the repair of bone defects is regulated by neural and vascular signals. In the present study, we examined the effect of topically applied β-nerve growth factor（β-NGF） on neurogenesis and angiogenesis in critical-sized bone defects filled with collagen bone substitute. We created two symmetrical defects, 2.5 mm in diameter, on either side of the parietal bone of the skull, and filled them with bone substitute. Subcutaneously implanted osmotic pumps were used to infuse 10 μgβ-NGF in PBS（β-NGF ＋ PBS） into the right-hand side defect, and PBS into the left（control） defect, over the 7 days following surgery. Immunohistochemical staining and hematoxylin-eosin staining were carried out at 3, 7, 14, 21 and 28 days postoperatively. On day 7, expression of β III-tubulin was lower on the β-NGF ＋ PBS side than on the control side, and that of neurofilament 160 was greater. On day 14, β III-tubulin and protein gene product 9.5 were greater on the β-NGF ＋ PBS side than on the control side. Vascular endothelial growth factor expression was greater on the experimental side than the control side at 7 days, and vascular endothelial growth factor receptor 2 expression was elevated on days 14 and 21, but lower than control levels on day 28. However, no difference in the number of blood vessels was observed between sides. Our results indicate that topical application of β-NGF promoted neurogenesis, and may modulate angiogenesis by promoting nerve regeneration in collagen bone substitute-filled defects.

Advanced Oxidation Protein Products Regulate the Pharmacokinetics of Aloe-emodin,Emodin,Rhein,and Chrysophanol in Chronic Kidney Disease Rats

Background:As accelerators and products of the progression of chronic kidney disease(CKD),advanced oxidation protein products(AOPPs)affect the function of the liver.Huang Gan granules(HGGs)are commonly used to prevent the progression of CKD,but the pharmacokinetics of aloe-emodin,emodin,rhein,and chrysophanol in HGGs in CKD remain unknown.Objective:To investigate the influence and its molecular mechanism of AOPPs on the in vivo pharmacokinetics of aloe-emodin,emodin,rhein,and chrysophanol in HGGs.Methods:We constructed 5/6 nephrectomised(5/6 nx),adenine-induced(adenine)and AOPP-treated rat models.After oral administration of HGG,the concentrations of aloe-emodin,emodin,rhein,and chrysophanol in the plasma samples were detected by high-performance liquid chromatography(HPLC),and their pharmacokinetics were analysed with the PKSolver software.The plasma concentrations of IL-6 and TNF-αare detected by enzyme linked immunosorbent assay(ELISA).The RT-PCR was performed in the HepG2 cells to explore the effect of TNF-αand IL-6 on the mRNA expression of CYP1A2 and CYP3A4.Result:The results showed that the method was suitable for the quantification of four anthraquinones in plasma and excreta samples with satisfactory linear(R R^(2)>0.9931),precision(<9.4%)and accuracy(±10%).In 5/6 nx,adenine and AOPPs-treated rats,the concentrations of TNF-αand IL-6 were increased.In 5/6 nx and adenine rats,the pharmacokinetic parameters(t_(1/2),MRT_(0-∞)and AUC_(0-∞))of aloe-emodin,emodin,rhein,and chryso-phanol were,respectively,significantly increased and correlated with the concentration of AOPPs.In AOPPs-treated rats,the concentration of AOPPs was significantly increased and the pharmacokinetic parameters of four anthraquinones were also increased.Conclusion:In summary,inflammatory cytokine production may be one of the important causes in AOPPs’regulat-ing the pharmacokinetic of aloe-emodin,emodin,rhein,and chrysophanol in the CKD rats.Studies of aloe-emodin,emodin,rhein,and chrysophanol in CKD facilitate the appropriate prescription of HGGs in the clinical.

Bioproduced Proteins On Demand(Bio-POD)in hydrogels using Pichia pastoris

Traditional production of industrial and therapeutic proteins by eukaryotic cells typically requires large-scale fermentation capacity.As a result,these systems are not easily portable or reusable for on-demand protein production applications.In this study,we employ Bioproduced Proteins On Demand(Bio-POD),a F127-bisurethane methacrylate hydrogel-based technique that immobilizes engineered Pichia pastoris for preservable,on-demand production and secretion of medium-and high-molecular weight proteins(in this case,SEAP,α-amylase,and anti-HER2).The gel samples containing encapsulated-yeast demonstrated sustained protein production and exhibited productivity immediately after lyophilization and rehydration.The hydrogel platform described here is the first hydrogel immobilization using a P.pastoris system to produce recombinant proteins of this breadth.These results highlight the potential of this formulation to establish a cost-effective bioprocessing strategy for on-demand protein production.

Advanced oxidation protein products induce monocyte chemoattractant protein-1 expression via p38 mitogen-activated protein kinase activation in rat vascular smooth muscle cells

Background Advanced oxidation protein products （AOPPs） are new uremic toxins reported by Witko-Sarsat in 1996, which are associated with the pathogenesis of atherosclerosis. However, the mechanisms by which AOPPs enhance atherosclerosis have not been fully understood. Monocyte chemoattractant protein-1 （MCP-1） is a chemokine which stimulates migration of monocytes and plays a critical role in the development of atherosclerosis. In this study, we investigated the effect of AOPPs on MCP-1 expression in cultured vascular smooth muscle cells （VSMCs）.

Specialized protein products in broiler chicken nutrition:A review

In poultry nutrition, most attention is given to protein products, due to the importance of protein as a major constituent of the biologically active compounds in the body. It also assists in the synthesis of body tissue, for that renovation and growth of the body. Furthermore, protein exists in form of enzymes and hormones which play important roles in the physiology of any living organism. Broilers have high dietary protein requirements, so identification of the optimum protein concentration in broiler diets, for either maximizing broiler performance or profit, requires more knowledge about birds' requirements for protein and amino acids and their effects on the birds' growth performance and development. It also requires knowledge about the protein sources available that can be used in poultry diets. The broad aim of this review is to highlight the importance of some of the available high-quality specialized protein products of both animal and plant origins which can be explored for feeding broiler chickens. Minimization of the concentration of anti-nutritional factors(ANFs) and supplementation with immunologically active compounds are the main focus of gut health-promoting broiler diets. These diet characteristics are influenced by feed ingredient composition and feed processing. The general hypothesis is that these protein products are highly digestible and devoid of or contain less ANFs. Feeding these products to broiler chicks, especially at an earlier age, can assist early gut development and digestive physiology, and improve broiler growth performance and immunity.

Advanced glycosylation end products, protein kinase C and renal alterations in diabetic rats

To study the relationship between advanced glycosylation end products (AGE) and protein kinase C (PKC), and their effects on renal alteration in diabetic rats Methods Insulin or aminoguanidine was administered to diabetic rats Blood glucose, hemoglobin A 1C (HbA 1C ), glomerular tissue extracts AGE (GTE AGE), PKC, glomerular basement membrane thickness (GBMT) and urine protein/creatinine (Pr/Cr) ratio in diabetic rats were measured and analysed Results Levels of blood glucose, HbA 1C and AGE, PKC activity, the Pr/Cr ratio and GBMT were all significantly increased ( P values all less than 0 01) in diabetic rats Insulin could decrease the formation of HbA 1C and AGE, and improve PKC activity Aminoguanidine had no influence on PKC activity ( P >0 05) although it decreased the formation of AGE Both drugs could delay the increase of urine Pr/Cr ratio and GBMT ( P <0 05 or P <0 01) Conclusions Chronic hyperglycemia may lead to an increase of PKC activity HbA 1C and AGE may not directly contribute to alterations of PKC activity, but the increase of PKC activity could promote the action of AGE on GBM thickening It is important to inhibit the formation of AGE and reduce the PKC activity so as to prevent or delay the development of diabetic nephropathy

Role of reactive oxygen species in the renal fibrosis

Renal fibrosis is a common pathway of progressive renal diseases leading to end-stage renal disease regardless of the etiology. Accumulating evidence indicates that oxidative stress, resulting in generation of reactive oxygen species （ROS）, plays a critical role in the initiation and progression of fibrotic diseases. Nicotinamide adenine dinucleotide phosphate （NADPH） oxidase is the predominant enzyme source for ROS generation and is now recognized as a key mediator of cell proliferation and matrix accumulation in renal disease. Multiple stimuli and agonists, such as transforming growth factor , tumor necrosis factor, platelet derived growth factor, angiotensin II, hyperglycemia, oxidized low-density lipoprotein and albumin have been shown to alter the activity or expression of the NADPH oxidase and ultimately increase ROS production. ROS directly incites damage to biologically important macromolecules and leads to generation of the so-called advanced oxidation protein products （AOPPs） and advanced glycation end products, which are not only markers of oxidative stress but also cause renal injury. Targeting NADPH oxidase and/or reducing AOPPs production miaht be a novel strateav for the theraoeutic intervention of varietv of fibrotic kidney disorders.