Search results for: protein sequences

Authors: Abdelsabour G. A. Khaled, Ahmed W. A. Abdalla And Sabry Y. M. Mahmoud

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Banana plants showing typical mosaic and yellow stripes on leaves as symptoms were collected from Assiut Governorate in Egypt. The causal agent was identified as Cucumber mosaic virus (CMV) on the basis of symptoms, transmission, serology, transmission electron microscopy and reverse transcription polymerase chain reaction (RT-PCR). Coat protein (CP) gene was amplified using gene specific primers for coat protein (CP), followed by cloning into desired cloning vector for sequencing. In this study the CMV was transmitted into propagation host either by aphid or mechanically. The transmission was confirmed through Direct Antigen Coating Enzyme Linked Immuno Sorbent Assay (DAC-ELISA). Analysis of the 120 deduced amino acid sequence of the coat protein gene revealed that the EG-A strain of CMV shared from 97.50 to 98.33% with those strains belonging to subgroup IA. The cluster analysis grouped the Egyptian isolate with strains Fny and Ri8 belonging sub-group IA. It appears that there occurs a high incidence of CMV infecting banana belonging to IA subgroup in most parts of Egypt.

Keywords: banana, CMV, transmission, CP gene, RT-PCR

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Authors: Saha Saradindu, Das Payel, Somdeb BoseDasgupta

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Tuberculosis caused by Mycobacteria tuberculosis is a dreadful disease and more so with the advent of extreme and total drug-resistant species. Mycobacterial pathogenesis is an ever-changing paradigm from phagosome maturation block to phagosomal escape into macrophage cytosol and finally acid tolerance and survival inside the lysosome. Mycobacteria are adept at subverting the host immune response by highjacking host cell signaling and secreting virulence factors. One such virulence factor is a ser/thr kinase; Protein kinase G (PknG), which is known to prevent phagosome maturation. The host substrates of PknG, allowing successful pathogenesis still remain an enigma. Hence we carried out a comparative phosphoproteomic screen and identified a number of substrates phosphorylated by PknG. We characterized some of these substrates in vivo and in vitro and observed that PknG mediated phosphorylation of these substrates leads to reduced TNFa production as well as decreased response to TNFa induced macrophage necroptosis, thus enabling mycobacterial survival and proliferation.

Keywords: mycobacteria, Protein kinase G, phosphoproteomics, necroptosis

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Authors: Khushi Kashyap, Pratibha Singh

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In the recent years increasing interest in vegetarian diets has been observed, a major problem in this type of diet is to provide the appropriate amount of protein .Value addition of food is current most talked topic because of increasing nutritional awareness among consumers today. An investigation was conducted to develop protein rich multi-millet hemp seed khakhra. The seeds of cannabis sativa L. have been a significant source of food for thousand of year. In recent years, hemp has not been thoroughly explored for its nutritional potential due to the mistaken belief regarding the cannabis plants. Methodology- two variations was prepared referencing standard recipe. Variation 1 was prepared using 25g ragi, 25g bajra,40g whole wheat flour with 10g hemp seed powder, variation 2(RF-25g,BF25g,WWF-35g,HS-15g). The product was subjected to sensory evolution by semi trained panel members using 9 point hedonic on 50 panelists. Result- result of the sensory evaluation revealed that the product incorporated with 15g of hemp seed were similar to control I texture, taste and overall quality and was more acceptable by the panelist and was selected as final product seed. On estimation of the nutrient content 30g of khakhra provides 107kcal of energy,12g protein,75g carbohydrate, and 9.6g of fats with shelf life of 3 months. Conclusion- khakhras can be eaten as a snack at any time of the day. hemp seed powder incorporated in it enhances its nutritive value and makes it more nutritious. It is suitable for consumption of all the age group.

Keywords: cannabis sativa, hemp, protein, seed

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Authors: Hung-Chieh Chen, Kuo-Hui Wang, Tsu-Lin Yeh

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Proteomics represent the performance of genomic complement proteins and the protein level on functional genomics. This study adopted proteomic strategies for comparing serum proteins among three groups: elite sprinter (sprint runner group, SR), long-distance runners (long-distance runner group, LDR), and the untrained control group (control group, CON). Purposes: This study aims to identify elite sprinters and long-distance runners’ serum protein and to provide a comparison of their serum proteome’ composition. Methods: Serum protein fractionations that separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and analyzed by a quantitative nano-LC-MS/MS-based proteomic profiling. The one-way analysis of variance (ANOVA) and Scheffe post hoc comparison (α= 0.05) was used to determine whether there is any significant difference in each protein level among the three groups. Results: (1) After analyzing the 307 identified proteins, there were 26 unique proteins in the SR group, and 18 unique proteins in the LDR group. (2) For the LDR group, 7 coagulation function-associated proteins’ expression levels were investigated: vitronectin, serum paraoxonase/arylesterase 1, fibulin-1, complement C3, vitamin K-dependent protein, inter-alpha-trypsin inhibitor heavy chain H3 and von Willebrand factor, and the findings show the seven coagulation function-associated proteins were significantly lower than the group of SR. (3) Comparing to the group of SR, this study found that the LDR group’s expression levels of the 2 antioxidant proteins (afamin and glutathione peroxidase 3) were also significantly lower. (4) The LDR group’s expression levels of seven immune function-related proteins (Ig gamma-3 chain C region, Ig lambda-like polypeptide 5, clusterin, complement C1s subcomponent, complement factor B, complement C4-A, complement C1q subcomponent subunit A) were also significantly lower than the group of SR. Conclusion: This study identified the potential serum protein markers for elite sprinters and long-distance runners. The changes in the regulation of coagulation, antioxidant, or immune function-specific proteins may also provide further clinical applications for these two different track athletes.

Keywords: biomarkers, coagulation, immune response, oxidative stress

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Authors: Olaide Ruth Aderibigbe, Oluwatoyin Oluwole

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Pigeon pea is one of the minor leguminous plants; though underutilised, it is used traditionally by farmers to alleviate hunger and malnutrition. Pigeon pea is cultivated in Nigeria by subsistence farmers. It is rich in protein and minerals, however, its utilisation as food is only common among the poor and rural populace who cannot afford expensive sources of protein. One of the factors contributing to its limited use is the high antinutrient content which makes it indigestible, especially when eaten by children. The development of value-added products that can reduce the antinutrient content and make the nutrients more bioavailable will increase the utilisation of the crop and contribute to reduction of malnutrition. This research, therefore, determined the effects of different roasting temperatures (130 0C, 140 0C, and 150 0C) on the proximate, mineral and antinutrient component of a pigeon pea snack. The brown variety of pigeon pea seeds were purchased from a local market- Otto in Lagos, Nigeria. The seeds were cleaned, washed, and soaked in 50 ml of water containing sugar and salt (4:1) for 15 minutes, and thereafter the seeds were roasted at 130 0C, 140 0C, and 150 0C in an electric oven for 10 minutes. Proximate, minerals, phytate, tannin and alkaloid content analyses were carried out in triplicates following standard procedures. The results of the three replicates were polled and expressed as mean±standard deviation; a one-way analysis of variance (ANOVA) and the Least Significance Difference (LSD) were carried out. The roasting temperatures significantly (P<0.05) affected the protein, ash, fibre and carbohydrate content of the snack. Ready-to-eat snack prepared by roasting at 150 0C significantly had the highest protein (23.42±0.47%) compared the ones roasted at 130 0C and 140 0C (18.38±1.25% and 20.63±0.45%, respectively). The same trend was observed for the ash content (3.91±0.11 for 150 0C, 2.36±0.15 for 140 0C and 2.26±0.25 for 130 0C), while the fibre and carbohydrate contents were highest at roasting temperature of 130 0C. Iron, zinc, and calcium were not significantly (P<0.5) affected by the different roasting temperatures. Antinutrients decreased with increasing temperature. Phytate levels recorded were 0.02±0.00, 0.06±0.00, and 0.07±0.00 mg/g; tannin levels were 0.50±0.00, 0.57±0.00, and 0.68±0.00 mg/g, while alkaloids levels were 0.51±0.01, 0.78±0.01, and 0.82±0.01 mg/g for 150 0C, 140 0C, and 130 0C, respectively. These results show that roasting at high temperature (150 0C) can be utilised as a processing technique for increasing protein and decreasing antinutrient content of pigeon pea.

Keywords: antinutrients, pigeon pea, protein, roasting, underutilised species

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Authors: Yue He, Youn Young Shim, Ji Hye Kim, Jae Youl Cho, Martin J. T. Reaney

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Recently, pulse cooking water (a.k.a. Aquafaba) has been used as an important and cost-effective alternative to eggs in gluten-free, vegan cooking and baking applications. The aquafaba (AQ) is primarily due to its excellent ability to stabilize foams and emulsions in foods. However, the functional ingredients of this excellent AQ are usually discarded with the compound release. This study developed a high-functional food material, AQ, using functional soybean AQ that has not been studied in Korea. A zero-waste and cost-effective hybrid process were used to produce oil emulsifiers from Korean soybeans. The treatment technique was implemented using a small number of efficient steps. Aquafaba from Backtae had the best emulsion properties (92%) and has the potential to produce more stable food oil emulsions. Therefore, this study is expected to be utilized in the development of the first gluten-free, vegan product for vegetarians and consumers with animal protein allergies, utilizing wastewater from cooked soybeans as a source of plant protein that can replace animal protein.

Keywords: aquafaba, soybean, chickpea, emulsifiers, egg replacer, egg-free products

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Authors: Jong Il Rhee

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The polypeptide representing the mature part of human BMP-7 was cloned and efficiently expressed in Escherichia coli and Bacillus subtilis, which had a clear band for hBMP-7, a homodimeric protein with an apparent molecular weight of 15.4 kDa. Recombinant E.coli produced 111 pg hBMP-7/mg of protein hBMP-7 through IPTG induction. Recombinant B. subtilis also produced 350 pg hBMP-7/ml of culture medium. The hBMP-7 was purified in 2 steps using an FPLC system with an ion exchange column and a gel filtration column. The hBMP-7 produced in this work also stimulated the alkaline phosphatase (ALP) activity in a dose-dependent manner, i.e. 2.5- and 8.9-fold at 100 and 300 ng hBMP-7/ml, respectively, and showed intact biological activity.

Keywords: B. subtilis, E. coli, fermentation, hBMP-7

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Authors: Priyanka Jain, Ashish K. Sharma, Esha Shukla, K. J. Mukherjee

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We propose a paradigm shift in our approach to design improved platforms for recombinant protein production, by addressing system level issues rather than the individual steps associated with recombinant protein synthesis like transcription, translation, etc. We demonstrate that by controlling and modulating the cellular stress response (CSR), which is responsible for feedback control of protein synthesis, we can generate hyper-producing strains. We did transcriptomic profiling of post-induction cultures, expressing different types of protein, to analyze the nature of this cellular stress response. We found significant down-regulation of substrate utilization, translation, and energy metabolism genes due to generation CSR inside the host cell. However, transcription profiling has also shown that many genes are up-regulated post induction and their role in modulating the CSR is unclear. We hypothesized that these up-regulated genes trigger signaling pathways, generating the CSR and concomitantly reduce the recombinant protein yield. To test this hypothesis, we knocked out the up-regulated genes, which did not have any downstream regulatees, and analyzed their impact on cellular health and recombinant protein expression. Two model proteins i.e., GFP and L-Asparaginase were chosen for this analysis. We observed a significant improvement in expression levels, with some knock-outs showing more than 7-fold higher expression compared to control. The 10 best single knock-outs were chosen to make 45 combinations of all possible double knock-outs. A further increase in expression was observed in some of these double knock- outs with GFP levels being highest in a double knock-out ΔyhbC + ΔelaA. However, for L-Asparaginase which is a secretory protein, the best results were obtained using a combination of ΔelaA+ΔcysW knock-outs. We then tested all the knock outs for their ability to enhance the expression of a 'difficult-to-express' protein. The Rubella virus E1 protein was chosen and tagged with sfGFP at the C-terminal using a linker peptide for easy online monitoring of expression of this fusion protein. Interestingly, the highest increase in Rubella-sGFP levels was obtained in the same double knock-out ΔelaA + ΔcysW (5.6 fold increase in expression yield compared to the control) which gave the highest expression for L-Asparaginase. However, for sfGFP alone, the ΔyhbC+ΔmarR knock-out gave the highest level of expression. These results indicate that there is a fair degree of commonality in the nature of the CSR generated by the induction of different proteins. Transcriptomic profiling of the double knock out showed that many genes associated with the translational machinery and energy biosynthesis did not get down-regulated post induction, unlike the control where these genes were significantly down-regulated. This confirmed our hypothesis of these genes playing an important role in the generation of the CSR and allowed us to design a strategy for making better expression hosts by simply knocking out key genes. This strategy is radically superior to the previous approach of individually up-regulating critical genes since it blocks the mounting of the CSR thus preventing the down-regulation of a very large number of genes responsible for sustaining the flux through the recombinant protein production pathway.

Keywords: cellular stress response, GFP, knock-outs, up-regulated genes

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Authors: Elena K. Schneider, Johnny X. Huang, Vincenzo Carbone, Mark Baker, Mohammad A. K. Azad, Matthew A. Cooper, Jian Li, Tony Velkov

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Ivacaftor is a novel CF trans-membrane conductance regulator (CFTR) potentiator that improves the pulmonary function for cystic fibrosis patients bearing a G551D CFTR-protein mutation. Because ivacaftor is highly bound (>97%) to plasma proteins, there is the strong possibility that co-administered CF drugs that compete for the same plasma protein binding sites and impact the free drug concentration. This in turn could lead to drastic changes in the in vivo efficacy of ivacaftor and therapeutic outcomes. This study compares the binding affinity of ivacaftor and co-administered CF drugs for human serum albumin (HSA) and α1-acid glycoprotein (AGP) using surface plasmon resonance and fluorimetric binding assays that measure the displacement of site selective probes. Due to their high plasma protein binding affinities, drug-drug interactions between ivacaftor are to be expected with ducosate, montelukast, ibuprofen, dicloxacillin, omeprazole and loratadine. The significance of these drug-drug interactions is interpreted in terms of the pharmacodynamic/pharmacokinetic parameters and molecular docking simulations. The translational outcomes of the data are presented as recommendations for a staggered treatment regimen for future clinical trials which aims to maximize the effective free drug concentration and clinical efficacy of ivacaftor.

Keywords: human α-1-acid glycoprotein, binding affinity, human serum albumin, ivacaftor, cystic fibrosis

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Authors: Thi Thao Ninh, Yuri Trusov, José Ramón Botella

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Heterotrimeric G proteins, comprised of three subunits, α, β and γ, are involved in signal transduction pathways that mediate a vast number of processes across the eukaryotic kingdom. 23 Gα subunits are present in humans whereas most plant genomes encode for only one canonical Gα. The disparity observed between Arabidopsis, rice, and maize Gα-deficient mutant phenotypes suggest that Gα functions have diversified between eudicots and monocots during evolution. Alternatively, since the only Gα mutations available in dicots have been produced in Arabidopsis, the possibility exists that this species might be an exception to the rule. In order to test this hypothesis, we studied the G protein α subunit (TGA1) in tomato. Four tga1 knockout lines were generated in tomato cultivar Moneymaker using CRISPR/Cas9. The tga1 mutants exhibit a number of auxin-related phenotypes including changes in leaf shape, reduced plant height, fruit size and number of seeds per fruit. In addition, tga1 mutants have increased sensitivity to abscisic acid during seed germination, reduced sensitivity to exogenous auxin during adventitious root formation from cotyledons and excised hypocotyl explants. Our results suggest that Gα mutant phenotypes in tomato are very similar to those observed in monocots, i.e. rice and maize, and cast doubts about the validity of using Arabidopsis as a model system for plant G protein studies.

Keywords: auxin-related phenotypes, CRISPR/Cas9, G protein α subunit, heterotrimeric G proteins, tomato

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Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

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Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system can facilitate targeted genome editing in organisms. Dual or single guide RNA (gRNA) can program the Cas9 nuclease to cut target DNA in particular areas; thus, introducing concise mutations either via error-prone non-homologous end-joining repairing or via incorporating foreign DNAs by homologous recombination between donor DNA and target area. In spite of high demand of such promising technology, developing a well-organized procedure in order for reliable mining of potential target sites for gRNAs in large genomic data is still challenging. Hence, we aimed to perform high-throughput detection of target sites by specific PAMs for not only common Streptococcus pyogenes (SpCas9) but also for Neisseria meningitides (NmCas9) CRISPR-Cas systems. Previous research confirmed the successful application of such RNA-guided Cas9 orthologs for effective gene targeting and subsequently genome manipulation. However, Cas9 orthologs need their particular PAM sequence for DNA cleavage activity. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of the target site for the two orthogonals of Cas9 protein, we created a reliable procedure to explore possible gRNA sequences. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. Finally, a complete list of all potential gRNAs along with their locations, strands, and PAMs sequence orientation can be provided for both SpCas9 as well as another potential Cas9 ortholog (NmCas9). The artificial design of potential gRNAs in a genome of interest can accelerate functional genomic studies. Consequently, the application of such novel genome editing tool (CRISPR/Cas technology) will enhance by presenting increased versatility and efficiency.

Keywords: CRISPR/Cas9 genome editing, gRNA mining, SpCas9, NmCas9

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Authors: Ashima Sharma

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Human Serum Albumin (HSA)- one of the most demanded therapeutic proteins with immense biotechnological applications- is a large multidomain protein containing 17 disulfide bonds. The current source of HSA is human blood plasma which is a limited and unsafe source. Thus, there exists an indispensable need to promote non-animal derived recombinant HSA (rHSA) production. Escherichia coli is one of the most convenient hosts which had contributed to the production of more than 30% of the FDA approved recombinant pharmaceuticals. It grows rapidly and reaches high cell density using inexpensive and simple substrates. E. coli derived recombinant products have more economic potential as fermentation processes are cheaper compared to the other expression hosts. The major bottleneck in exploiting E. coli as a host for a disulfide-rich multidomain protein is the formation of aggregates of overexpressed protein. The majority of the expressed HSA forms inclusion bodies (more than 90% of the total expressed rHSA) in the E. coli cytosol. Recovery of functional rHSA from inclusion bodies is not preferred because it is difficult to obtain a large multidomain disulfide bond rich protein like rHSA in its functional native form. Purification is tedious, time-consuming, laborious and expensive. Because of such limitations, the E. coli host system was neglected for rHSA production for the past few decades despite its numerous advantages. In the present work, we have exploited the capabilities of E. coli as a host for the enhanced functional production of rHSA (~60% of the total expressed rHSA in the soluble fraction). Parameters like intracellular environment, temperature, induction type, duration of induction, cell lysis conditions etc. which play an important role in enhancing the level of production of the desired protein in its native form in vivo have been optimized. We have studied the effect of assistance of different types of exogenously employed chaperone systems on the functional expression of rHSA in the E. coli host system. Different aspects of cell growth parameters during the production of rHSA in presence and absence of molecular chaperones in E. coli have also been studied. Upon overcoming the difficulties to produce functional rHSA in E. coli, it has been possible to produce significant levels of functional protein through engineering the biological system of protein folding in the cell, the E. coli-derived rHSA has been purified to homogeneity. Its detailed physicochemical characterization has been performed by monitoring its conformational properties, secondary and tertiary structure elements, surface properties, ligand binding properties, stability issues etc. These parameters of the recombinant protein have been compared with the naturally occurring protein from the human source. The outcome of the comparison reveals that the recombinant protein resembles exactly the same as the natural one. Hence, we propose that the E. coli-derived rHSA is an ideal biosimilar for human blood plasma-derived serum albumin. Therefore, in the present study, we have introduced and promoted the E. coli- derived rHSA as an alternative to the preparation from a human source, pHSA.

Keywords: recombinant human serum albumin, Escherichia coli, biosimilar, chaperone assisted protein folding

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Authors: Chaoran Liu

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Bioactive polysaccharides and polysaccharide-protein complex derived from mushrooms and fungi have a wide range of immunomodulatory activity with low side-effects and have therefore the potential to be developed as an adjuvant in cancer therapies. Mushrooms sclerotium is rich in polysaccharides and the polysaccharides isolated from the sclerotium of Polyporus rhinocerus have shown potent in vivo and in vitro immunomodulatory effects. Macrophages are considered to be an important component of the innate immune response against bacterial infection and cancer. To better understanding the immunomodulatory effects and its underlying mechanisms of sclerotial water-soluble polysaccharides extracted from P. rhinocerus on macrophages, the objectives of this study are to purify the water-soluble novel sclerotial polysaccharides and to characterize the structure and properties as well as to study the detailed molecular mechanisms of the in vitro immunomodulating effects in murine macrophages. The hot water-soluble fraction PRW from the sclerotium of P. rhinocerus was obtained using solvent extraction. PRW was further fractionated by membrane ultrafiltration to a give a fraction (PRW1) with molecular mass less than 50 kDa. PRW1 was characterized to be a polysaccharide-protein complex composed of 45.7% polysaccharide and 44.2% protein. The chemical structure of the carbohydrate moiety of PRW1 was elucidated by GC and FTIR to be mainly beta-D-glucan with trace amount of galactose and mannose. The immunomodulatory effects of PRW1 on murine RAW 264.7 macrophages were demonstrated in terms of the increase in nitric oxide production and cytokine production. Mechanistically, PRW1 initiates ERK phosphorylation to activate macrophages within 15 min and significantly improves the expression level of inducible NOS (iNOS) from 6 h after treatment. In summary, this study indicates that PRW1 is a potent immunomodulatory agent for macrophages and suggests that mushroom sclerotia from Polyporus rhinocerus requires for further investigation in cancer research.

Keywords: Polyporus rhinocerus, mushroom sclerotia, Polysaccharide-Protein Complex, macrophage activation

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Authors: Ebraheem Al-Jouri, Youssef Abu-Ahmad, Ramasamy Srinivasan

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The parasitoid, Diadegma semiclausum (Hymenoptera: Ichneumonidae) is one of the most effective exotic parasitoids of diamondback moth (DBM), Plutella xylostella in the lowland areas of Homs, Syria. Molecular evolution studies are useful tools to shed light on the molecular bases of insect geographical spread and adaptation to new hosts and environment and for designing better control strategies. In this study, molecular evolution analysis was performed based on the 42 nuclear internal transcribed spacer-2 (ITS2) sequences representing the D. semiclausum and eight other Diadegma spp. from Syria and worldwide. Possible recombination events were identified by RDP4 program. Four potential recombinants of the American D. insulare and D. fenestrale (Jeju) were detected. After detecting and removing recombinant sequences, the ratio of non-synonymous (dN) to synonymous (dS) substitutions per site (dN/dS=ɷ) has been used to identify codon positions involved in adaptive processes. Bayesian techniques were applied to detect selective pressures at a codon level by using five different approaches including: fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL), random effects method (REL), mixed effects model of evolution (MEME) and Program analysis of maximum liklehood (PAML). Among the 40 positively selected amino acids (aa) that differed significantly between clades of Diadegma species, three aa under positive selection were only identified in D. semiclausum. Additionally, all D. semiclausum branches tree were highly found under episodic diversifying selection (EDS) at p≤0.05. Our study provide evidence that both recombination and positive selection have contributed to the molecular diversity of Diadegma spp. and highlights the significant contribution of D. semiclausum in adaptive evolution and influence the fitness in the DBM parasitoid.

Keywords: diadegma sp, DBM, ITS2, phylogeny, recombination, dN/dS, evolution, positive selection

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Authors: Swati Srivastava, Ashish Kumar Upadhyay

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Using longitudinal data from three waves of Young Lives Study and Ordinary Least Square methods, study has investigated the effect of birth order and arrival of younger siblings on child development in India. Study used child’s height for age z-score, weight for age z-score, BMI for age z-score, Peabody Picture Vocabulary Test (PPVT-Score)c, maths score, Early Grade Reading Assessment Test (ERGA) score, and memory score to measure the physical and cognitive development of child during wave-3. Findings suggest that having a high birth order is detrimental for child development and the gap between adjacent siblings is larger for children late in the birth sequences than early in the birth sequences. Study also reported that not only older siblings but arrival of younger siblings before assessment of test also reduces the development of a child. The effects become stronger in case of female children than male children.

Keywords: height for age z-score, weight for age z-score, BMI for z-score, PPVT score, math score, EGRA score, memory score, birth order, siblings, Young Lives Study, India

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Authors: Reena Murali, David Peter S.

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The small interfering RNA (siRNA) alters the regulatory role of mRNA during gene expression by translational inhibition. Recent studies shows that up regulation of mRNA cause serious diseases like Cancer. So designing effective siRNA with good knockdown effects play an important role in gene silencing. Various siRNA design tools had been developed earlier. In this work, we are trying to analyze the existing good scoring second generation siRNA predicting tools and to optimize the efficiency of siRNA prediction by designing a computational model using Artificial Neural Network and whole stacking energy (ΔG), which may help in gene silencing and drug design in cancer therapy. Our model is trained and tested against a large data set of siRNA sequences. Validation of our results is done by finding correlation coefficient of experimental versus observed inhibition efficacy of siRNA. We achieved a correlation coefficient of 0.727 in our previous computational model and we could improve the correlation coefficient up to 0.753 when the threshold of whole tacking energy is greater than or equal to -32.5 kcal/mol.

Keywords: artificial neural network, double stranded RNA, RNA interference, short interfering RNA

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Authors: Kayode O. Afolabi, Benson C. Iweriebor, Anthony I. Okoh, Larry C. Obi

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Porcine circovirus type 2 (PCV2) is the major etiological viral agent of porcine multisystemic wasting syndrome (PWMS) and other porcine circovirus-associated diseases (PCVAD) of great economic importance in pig industry globally. In an effort to determine the status of swine herds in the Province as regarding the ‘small but powerful’ viral pathogen; a total of 375 blood, faecal and nasal swab samples were obtained from seven pig farms (commercial and communal) in Amathole, O.R. Tambo and Chris-Hani District Municipalities of Eastern Cape Province between the year 2015 and 2016. Three hundred and thirty nine (339) samples out of the total sample were subjected to molecular screening using PCV2 specific primers by conventional polymerase chain reaction (PCR). Selected sequences were further analyzed and confirmed through genome sequencing and phylogenetic analyses. The data obtained revealed that 15.93% of the screened samples (54/339) from the swine herds of the studied areas were positive for PCV2; while the severity of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6% to 60% in the studied farms. The Majority, precisely 15 out of 17 (88%) analyzed sequences were found clustering with other PCV2b reference strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genogroup, which is presently another fast-spreading genotype with observable higher virulence in global swine herds. This finding confirmed the presence of this all-important viral pathogen in pigs of the region; which could result in a serious outbreak of PCVAD and huge economic loss at the instances of triggering factors if no appropriate measures are taken to curb its spread effectively.

Keywords: pigs, polymerase chain reaction, porcine circovirus type 2, South Africa

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Authors: Tagouelbe Tiho, Amissa Augustin Adima, Yao Casimir Brou, Nabayo Traore, Gouha Firmin Kouassi, Thierry Roland Kouame, Maryline Kouba

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The work aimed to study Borassus aethiopum Mart (B.a) dried pulp nutritional value for its incorporation in human and poultry diets. Firstly, the mature fruit macro-composition was assessed. Secondly, the pulp was dried at 40, 50, 60, 70, and 80ᵒC. Thereafter, the analysis was performed for fat, protein, total sugars, Ca, P, Mg, and fatty acid profile monitoring. As a result, the fruits weighed 1,591.35, delivered 516.73, and 677.82 grams of pulp and seeds, respectively. Mainly, increasing heat adversely affected the outputs. Consequently, the fat results were 14.12, 12.97, 8.93, 8.89ᶜ, and 5.56%; protein contents were 11.64, 10.15, 8.97, 8.84, and 8.42%; total sugar deliveries were 6.28, 6.05, 5.26, 5.02, and 4.76% (P < 0.01). Thereafter, the metabolizable energies were 3,785.22; 3,834.28; 3,616.62; 3,667.03; and 3,608.33 kcal/kg (DM). Additionally, Calcium (Ca) contents were 0.51, 0.55, 0.69, 0.77, and 0.81%, while phosphorus (P) mean was 0.17%, and the differences were not significant (P < 0.01). So, the Ca/P ratios were 2.79, 3.04, 4.10, 4.71, and 4.95. Finally, fatty acids (FA) assessments revealed 22.33 saturated (SFA), 77.67 unsaturated (UFA), within which 67.59% were monounsaturated (MUFA). Interestingly, the rising heat depressed n-6/n-3 ratios that were 1.1, 1.1, 0.45 and 0.38, respectively at 40, 50, 70 and 80ᵒC. In short, drying did not only enhance the product shelf life but it also improved the nutritional value. Thus, B.a mature fruit pulps dried at 70ᵒC are good functional foods, with more than 66% MUFA, and energy source for human and poultry nutrition.

Keywords: Borassus aethiopum Mart, fatty acids, metabolizable energy, minerals, protein

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Authors: M. Michael Gromiha, A. Mary Thangakani, Sandeep Kumar, D. Velmurugan

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The main cause of several neurodegenerative diseases such as Alzhemier, Parkinson, and spongiform encephalopathies is formation of amyloid fibrils and plaques in proteins. We have analyzed different sets of proteins and peptides to understand the influence of sequence-based features on protein aggregation process. The comparison of 373 pairs of homologous mesophilic and thermophilic proteins showed that aggregation-prone regions (APRs) are present in both. But, the thermophilic protein monomers show greater ability to ‘stow away’ the APRs in their hydrophobic cores and protect them from solvent exposure. The comparison of amyloid forming and amorphous b-aggregating hexapeptides suggested distinct preferences for specific residues at the six positions as well as all possible combinations of nine residue pairs. The compositions of residues at different positions and residue pairs have been converted into energy potentials and utilized for distinguishing between amyloid forming and amorphous b-aggregating peptides. Our method could correctly identify the amyloid forming peptides at an accuracy of 95-100% in different datasets of peptides.

Keywords: aggregation, amyloids, thermophilic proteins, amino acid residues, machine learning techniques

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Authors: Natela Gerliani, Mohammed Aider

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Nowadays, the interest of using sustainable technologies for protein extraction from underutilized oilseeds is growing. Currently, a major disposal problem for the oil industry is by-products of plant food processing such as soybean meal. That is why valorization of soybean meal is important for the oil industry since it contains high-quality proteins and other valuable components. Generally, soybean meal is used in livestock and poultry feed but is rarely used in human feed. Though chemical composition of this meal compensate nutritional deficiency and can be used to balance protein in human food. Regarding the efficiency of soybean meal valorization, extraction is a key process for obtaining enriched protein ingredient, which can be incorporated into the food matrix. However, most of the food components such as proteins extracted from oilseeds by-products imply the utilization of organic and inorganic chemicals (e.g. acids, bases, TCA-acetone) having a significant environmental impact. In a context of sustainable production, the use of an electro-activation technology seems to be a good alternative. Indeed, the electro-activation technology requires only water, food grade salt and electricity as main materials. Moreover, this innovative technology helps to avoid special equipment and trainings for workers safety as well as transport and storage of hazardous materials. Electro-activation is a technology based on applied electrochemistry for the generation of acidic and alkaline solutions on the basis of the oxidation-reduction reactions that occur at the vicinity electrode/solution interfaces. It is an eco-friendly process that can be used to replace the conventional acidic and alkaline extraction. In this research, the electro-activation technology for protein extraction from soybean meal was carried out in the electro-activation reactor. This reactor consists of three compartments separated by cation and anion exchange membranes that allow creating non-contacting acidic and basic solutions. Different current intensities (150 mA, 300 mA and 450 mA) and treatment durations (10 min, 30 min and 50 min) were tested. The results showed that the extracts obtained by the electro-activation method have good quality in comparison to conventional extracts. For instance, extractability obtained with electro-activation method was 55% whereas with the conventional method it was only 36%. Moreover, a maximum protein quantity of 48 % in the extract was obtained with the electro-activation technology comparing to the maximum amount of protein obtained by conventional extraction of 41 %. Hence, the environmentally sustainable electro-activation technology seems to be a promising type of protein extraction that can replace conventional extraction technology.

Keywords: by-products, eco-friendly technology, electro-activation, soybean meal

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Authors: Abdu Umar Adamu, Saidu Akun Abdullahi, Al-Hassan Muhammed, Hamisu Abdu

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Leguminous plants such as beans have been considered as a source of protein in this present work. The proximate analysis on beans (Vigna unguiculata) were determined in order to identify the nutritional content as well as presence of some heavy metals accumulation in washed and unwashed beans (white Beans) sold in Kazaure market Jigawa State Nigeria. On the average comparative analysis, the result has indicated that, the Vigna unguiculata had protein content of 61.1%, fibre 4.5%, ash 10.4%, moisture 5%, carbohydrate 15.8% and total lipid 4.9%, therefore it could be suggested that beans has enough nutritional content that helps the people health. The heavy metal analysis of unwashed white beans showed that Fe (17.37 ± 6.71)mg/kg had the highest concentration followed by Zn (6.41 ± 3.09), Cu (5.69 ± 2.42), Cd (0.46 ± 0.65) and Pb (0.57 ± 0.94)mg/kg , while the washed beans shows that Zn (0.11 ± 0.17), Fe (0.01 ± 0.006), Cd (0.02 ± 0.01), Cu (0.03 ± 0.021), Pb (0.01 ± 0.006)mg/kg. The washed white beans are safe for consumption and also the concentration of heavy metal are negligible and of nontoxic effect to human health.

Keywords: white beans, protein, proximate composition, heavy metal

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Authors: Ruolan Zhou

Abstract:

Trisomy of human chromosome 21 is the primary cause of Down Syndrome (DS), and this genetic disease has significantly burdened families and countries, causing great controversy. To address this problem, the research takes an approach in exploring the relationship between genetic abnormality and this disease's symptoms, adopting several techniques, including data analysis and enrichment analysis. It also explores open-source websites, such as NCBI, DAVID, SOURCE, STRING, as well as UCSC, to complement its result. This research has analyzed the variety of genes on human chromosome 21 with simple coding, and by using analysis, it has specified the protein-coding genes, their function, and their location. By using enrichment analysis, this paper has found the abundance of keratin production-related coding-proteins on human chromosome 21. By adopting past researches, this research has attempted to disclose the relationship between trisomy of human chromosome 21 and keratin production abnormality, which might be the reason for common diseases in patients with Down Syndrome. At last, by addressing the advantage and insufficiency of this research, the discussion has provided specific directions for future research.

Keywords: Down Syndrome, protein production, genome, enrichment analysis

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Authors: Anjum-Zubair, Muhammad, Muhammad Shoaib Alam, Muhammad Samee Mubarik, Iftikhar Ahmad

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The aim of present research was to evaluate the effect of dietary protein (soybean) formulated feed on the growth performance of carp fish seed (Rohu, Mori, Grass, and Gulfam) in ponds under polyculture system. Keeping in view the protein requirements of these four carps, they were fed with formulated feed contains 30% of crude protein. The fingerlings were fed once on daily basis at 5% of their wet body weight. A 90 days experiment was conducted in two cemented ponds situated at Fish Seed Hatchery and Research Centre, Rawal Town, Islamabad, Pakistan. Pond1 contain major carps i.e. Rohu and Mori while pond 2 was stocked with Chinese carps i.e. Grass carp and Gulfam. Random sampling of five individuals of each species was done fortnightly to measure the body weight and total body length. Maximum growth was observed in fingerling of Grass carp followed by Mori, Rohu and Gulfam. Total fish production was recorded as Grass 623.45 gm followed by Mori 260.3 gm, Rohu 243.08 gm and Gulfam 181.165 gm respectively. Significantly results were obtained among these four fish species when the corresponding data was subjected to statistical analysis by using two sample t-test. The survival rate was 100%. Study shows that soybean as plant based protein can be easily used as substitute to fish meal without any adverse effect on fish health and fish production.

Keywords: carps, fry growth, poly culture, soybean meal

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Authors: A. Ojha, Y. K. Gupta

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Organophosphate (OP) pesticides are among the most widely used synthetic chemicals for controlling a wide variety of pests throughout the world. Chlorpyrifos (CPF), methyl parathion (MPT), and malathion (MLT) are among the most extensively used OP pesticides in India. DNA strand breaks and DNA-protein crosslinks (DPC) are toxic lesions associated with the mechanisms of toxicity of genotoxic compounds. In the present study, we have examined the potential of CPF, MPT, and MLT individually and in combination, to cause DNA strand breakage and DPC formation. Peripheral blood lymphocytes of rat were exposed to 1/4 and 1/10 LC50 dose of CPF, MPT, and MLT for 2, 4, 8, and 12h. The DNA strand break was measured by the comet assay and expressed as DNA damage index while DPC estimation was done by fluorescence emission. There was significantly marked increase in DNA damage and DNA-protein crosslink formation in time and dose dependent manner. It was also observed that MPT caused the highest level of DNA damage as compared to other studied OP compounds. Thus, from present study, we can conclude that studied pesticides have genotoxic potential. The pesticides mixture does not potentiate the toxicity of each other. Nonetheless, additional in vivo data are required before a definitive conclusion can be drawn regarding hazard prediction to humans.

Keywords: organophosphate, pesticides, DNA damage, DNA protein crosslink, genotoxic

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Authors: Hyun-Koo Kim, Yong-Hun Kim, Soo-Young Suk, Ju H. Park, Ho-Youl Jung

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This paper presents an effective speed hump detection process at the day-time. we focus only on round types of speed humps in the day-time dynamic road environment. The proposed speed hump detection scheme consists mainly of two process as stereo matching and speed hump detection process. Our proposed process focuses to speed hump detection process. Speed hump detection process consist of noise reduction step, data fusion step, and speed hemp detection step. The proposed system is tested on Intel Core CPU with 2.80 GHz and 4 GB RAM tested in the urban road environments. The frame rate of test videos is 30 frames per second and the size of each frame of grabbed image sequences is 1280 pixels by 670 pixels. Using object-marked sequences acquired with an on-vehicle camera, we recorded speed humps and non-speed humps samples. Result of the tests, our proposed method can be applied in real-time systems by computation time is 13 ms. For instance; our proposed method reaches 96.1 %.

Keywords: data fusion, round types speed hump, speed hump detection, surface filter

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Authors: Izzatul Ulfana, Angga Pratomo Cahyadi, Rimayanti, Widjiati

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Freezing oocyte could cause temperature stress. Temperature stress triggers cell damage. Insulin Transferrin Selenium (ITS) and Heat Shock Protein 70 (HSP70) had been used to prevent damage to the oocyte after freezing. ITS and HSP70 could cause the difference protective effect. The aim of this research was to obtain an effective cryoprotectant for freezing local goat oocyte in cumulus cells change. The research began by collecting the ovary from a local slaughterhouse in Indonesia, aspiration follicle, in vitro maturation and the freezing had been used vitrification method. Examination of the morphology cells by native staining method. Data on the calculation morphology oocyte analyzed by Kruskall-Wallis Test. After the Kruskall-Wallis Test which indicated significance, followed by Mann-Whitney Test to compare between treatment groups. As a result, cryoprotectant ITS has the best culumus cells after warming

Keywords: Insulin Transferrin Selenium, Heat Shock Protein 70, cryoprotectant, vitrification

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Authors: Jiraporn Rojtinnakorn

Abstract:

ICAM-2 (intercellular adhesion molecule 2) or CD102 (Cluster of Differentiation 102) is type I trans-membrane glycoproteins, composing 2-9 immunoglobulin-like C2-type domains. ICAM-2 plays the particular role in immune response and cell surveillance. It is concerned in innate and specific immunity, cell survival signal, apoptosis, and anticancer. EST clone of ICAM-2, from P. gigas blood cell EST libraries, showed high identity to human ICAM-2 (92%) with conserve region of ICAM N-terminal domain and part of Ig superfamily. Gene and protein of ICAM-2 has been founded in mammals. This is the first report of ICAM-2 in fish.

Keywords: ICAM-2, CD102, Pangasianodon gigas, antitumor

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Authors: Ishaq Kashif, Muhammad Younas, Muhammad Riaz, Mubarak Ali

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Poor feeding management during pre-weaning period is one of the factors resulting in compromised growth of Beetal kids fattened for meat purpose. The main reason for this anomaly may be less milk offered to kids and non-serious efforts for its management. This study was planned to find the most appropriate protein level suiting the age of the weaning while shifting animals to high input feeding system. Total of 42 Beetal male kids having 30 (±10), 60 (±10) and 90 (±10) days of age were selected with 16 in each age group. They were designated as G30, G60 and G90, respectively. The weights of animals were; 8±2 kg (G30), 12±2 kg (G60) and 16±2 kg (G90), respectively. All animals were weaned by introducing the total mix feed gradually and withdrawing the milk during the adjustment period of two weeks. The pelleted starter ration (total mix feed) with three various dietary protein levels designated as R1 (16% CP), R2 (20% CP) and R3 (26% CP) were introduced. The control group was reared on the fodder (Maize). The starter rations were iso-caloric and were offered for six-week duration. All animals were exposed to treatment using two-factor factorial (3×3) plus control treatment arrangement under completely randomized design. The data were collected on average daily feed intake (ADFI), average daily gain (ADG), gain to intake ratio, Klieber ratio (KR), body measurements and blood metabolites of kids. The data was analyzed using aov function of R-software. The statistical analysis showed that starter feed protein levels and age of weaning had significant interaction for ADG (P < 0.001), KR (P < 0.001), ADFI (P < 0.05) and blood urea nitrogen (P < 0.05) while serum creatinine and feed conversion had non-significant interaction. The trend analysis revealed that ADG had significant quadratic interaction (P < 0.05) within protein levels and age of weaning. It was found that animals weaned at 30 or 60 days, on R2 diet had better ADG (46.8 gm/day and 87.06 gm/day, respectively) weaned at 60 days of age. The animals weaned at 90 days had best ADG (127 gm/day) with R1. It is concluded that animal weaned at 30 or 40 days required 20% CP for better growth performance while animal at 90 days showed better performance with 16% CP.

Keywords: average daily gain, starter protein levels, weaning age, gain to intake ratio

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Authors: Alexander Vandesompele, Joni Dambre

Abstract:

The diversity in dendritic arborization, as first illustrated by Santiago Ramon y Cajal, has always suggested a role for dendrites in the functionality of neurons. In the past decades, thanks to new recording techniques and optical stimulation methods, it has become clear that dendrites are not merely passive electrical components. They are observed to integrate inputs in a non-linear fashion and actively participate in computations. Regardless, in simulations of neural networks dendritic structure and functionality are often overlooked. Especially in a machine learning context, when designing artificial neural networks, point neuron models such as the leaky-integrate-and-fire (LIF) model are dominant. These models mimic the integration of inputs at the neuron soma, and ignore the existence of dendrites. In this work, the LIF point neuron model is extended with a simple form of dendritic computation. This gives the LIF neuron increased capacity to discriminate spatiotemporal input sequences, a dendritic functionality as observed in another study. Simulations of the spiking neurons are performed using the Bindsnet framework. In the common LIF model, incoming synapses are independent. Here, we introduce a dependency between incoming synapses such that the post-synaptic impact of a spike is not only determined by the weight of the synapse, but also by the activity of other synapses. This is a form of short term plasticity where synapses are potentiated or depressed by the preceding activity of neighbouring synapses. This is a straightforward way to prevent inputs from simply summing linearly at the soma. To implement this, each pair of synapses on a neuron is assigned a variable,representing the synaptic relation. This variable determines the magnitude ofthe short term plasticity. These variables can be chosen randomly or, more interestingly, can be learned using a form of Hebbian learning. We use Spike-Time-Dependent-Plasticity (STDP), commonly used to learn synaptic strength magnitudes. If all neurons in a layer receive the same input, they tend to learn the same through STDP. Adding inhibitory connections between the neurons creates a winner-take-all (WTA) network. This causes the different neurons to learn different input sequences. To illustrate the impact of the proposed dendritic mechanism, even without learning, we attach five input neurons to two output neurons. One output neuron isa regular LIF neuron, the other output neuron is a LIF neuron with dendritic relationships. Then, the five input neurons are allowed to fire in a particular order. The membrane potentials are reset and subsequently the five input neurons are fired in the reversed order. As the regular LIF neuron linearly integrates its inputs at the soma, the membrane potential response to both sequences is similar in magnitude. In the other output neuron, due to the dendritic mechanism, the membrane potential response is different for both sequences. Hence, the dendritic mechanism improves the neuron’s capacity for discriminating spa-tiotemporal sequences. Dendritic computations improve LIF neurons even if the relationships between synapses are established randomly. Ideally however, a learning rule is used to improve the dendritic relationships based on input data. It is possible to learn synaptic strength with STDP, to make a neuron more sensitive to its input. Similarly, it is possible to learn dendritic relationships with STDP, to make the neuron more sensitive to spatiotemporal input sequences. Feeding structured data to a WTA network with dendritic computation leads to a significantly higher number of discriminated input patterns. Without the dendritic computation, output neurons are less specific and may, for instance, be activated by a sequence in reverse order.

Keywords: dendritic computation, spiking neural networks, point neuron model

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Authors: Eitedal Daoud, Reda M.Daoud, Khaled Abdel-Wahhab, Maha M.Saber, Lobna Saber

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Background: Cis-platin is a widely used chemotherapeutic drug to treat many malignant disorders including head and neck malignancies. Oto-nephrotxicity is an important and dose - limiting side effect of cis - platin therapy. Nowadays, more attention had been paid to oto-toxicity caused with cis-platin. Aim of the Work: This study was designed to investigate the potential protective effect of Whey protein (WP) against cis-platin induced ototoxicity compared to the effect of N-acetylcysteine (NAC) in rats. Methodology: Male albino rats were randomly divided into 6 groups: untreated rats (control), rats orally treated with whey protein (1g/kg b.w/day) for seven executive days, rats treated orally with N-acetylcysteine (500 mg/kgb.w /day) for seven executive days, rates intoxicated intraperitoneal (ip) with cis- platin (10 mg/kgb.w. once), rats treated with whey protein (1g/kgb.w./day) for seven executive days) followed by one injection (ip) of cis-platin(10 mg/kg b.w.) one hour after the last oral administration of whey protein, rats treated with N- acetylcysteine (for seven executive days followed by one injection (ip) of cis-platin (10 mg/kgb.w) one hour after the last oral administration of N-acetylcysteine. The organ of Corti, the stria vascularis and spiral ganglia were visualized by light microscopy at different magnifications. Results: Cis-platin intoxicated animals showed a significant decrease in serum level of total antioxidant capacity (TAC),with inhibition in the activity of serum glutathione-s transferase(GST) and paraoxonnase-1 (PON-1) in comparison with control. Group treated with either NAC or WP with cis-platin showed significant elevation in the activity of both GST & PON-1 with increased serum level of TAC when compared with cis-platin intoxicated rats. Animals treated with NAC or WP with cis-platin compared to those treated with cis-platin alone showed marked degree of improvement towards control rats as there was significant drop in the serum level of cortecosterone, nitric oxide (NO), and melandialdehyde (MDA).Histopathologic, in NAC pretreated group there was no changes in stria vascularis or spiral ganglia. In group pretreated with WP, there was no histopathologic alteration detected in the organ of Corti and Reissers membrane but oedema and haemorrhage were founded in the stria vascularis in small focal manner. Conclusion: Our finding showed that Whey protein is a natural dietary supplement product proved its ability of protection of anti-oxidant system and the cochlea against cis-platin induced ototoxicity.

Keywords: anti-oxidant, cis-platin, N-acetylcysteine, ototoxicity, whey protein

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