Search results for: therapeutic protein analysis

Authors: Klaudia Chmielewska, Krystyna Dzierzbicka, Iwona Inkielewicz-Stepniak

Abstract:

Carnosine, an endogenous peptide consisting of β-alanine and L-histidine has a variety of functions to mention: antioxidant, antiglycation, and reducing the toxicity of metal ions. It has therefore been proposed to act as a therapeutic agent for many pathological states, although its therapeutic index is limited by quick enzymatic cleavage. To overcome this limitation, there’s an urge to create new derivatives which might become less potent to hydrolysis, while preserving the therapeutic effect. The poster summarizes the efficiency of two peptide synthesis methods, which were: (1) the mixed anhydride with isobutyl chloroformate and N-methylmorpholine (NMM) and (2) carbodiimide - mediated coupling method via appropriate reagent condensing, here – CDI. The methods were used to obtain dipeptides which were the derivatives of carnosine. Obtained dipeptides were made in the form of methyl esters and their structures will be confirmed 1H NMR, 13C NMR, MS and elemental analysis techniques. Later on, they will be analyzed for their antioxidant properties, in comparison to carnosine.

Keywords: carnosine, method, peptide, synthesis

Procedia PDF Downloads 126

Authors: Farideh Halakou, Emel Sen, Attila Gursoy, Ozlem Keskin

Abstract:

Protein–Protein Interactions (PPIs) mediate major biological processes in living cells. The study of PPIs as networks and analyze the network properties contribute to the identification of genes and proteins associated with diseases. In this study, we have created the sub-networks of brain and lung metastasis from primary tumor in breast cancer. To do so, we used seed genes known to cause metastasis, and produced their interactions through a network-topology based prioritization method named GUILDify. In order to have the experimental support for the sub-networks, we further curated them using STRING database. We proceeded by modeling structures for the interactions lacking complex forms in Protein Data Bank (PDB). The functional enrichment analysis shows that KEGG pathways associated with the immune system and infectious diseases, particularly the chemokine signaling pathway, are important for lung metastasis. On the other hand, pathways related to genetic information processing are more involved in brain metastasis. The structural analyses of the sub-networks vividly demonstrated their difference in terms of using specific interfaces in lung and brain metastasis. Furthermore, the topological analysis identified genes such as RPL5, MMP2, CCR5 and DPP4, which are already known to be associated with lung or brain metastasis. Additionally, we found 6 and 9 putative genes that are specific for lung and brain metastasis, respectively. Our analysis suggests that variations in genes and pathways contributing to these different breast metastasis types may arise due to change in tissue microenvironment. To show the benefits of using structural PPI networks instead of traditional node and edge presentation, we inspect two case studies showing the mutual exclusiveness of interactions and effects of mutations on protein conformation which lead to different signaling.

Keywords: breast cancer, metastasis, PPI networks, protein conformational changes

Procedia PDF Downloads 209

Authors: Sodamade A., Bolaji K. A.

Abstract:

Problems associated with protein malnutrition are still prevalent in third-world countries, leading to the constant search for plants that could serve as nutrients and medicinal purposes. Huckleberry is one of the plants that has been proven useful locally in the treatment of numerous ailments and diseases. A fresh sample of the plant (Vaccinium pavifolium) was collected from a vegetable garden situated near the Erelu dam of the Emmanuel Alayande College of Education Campus, Oyo. The sample was authenticated at the Forestry Research Institute of Nigeria (FRIN) Ibadan. The leaves of the plant were plucked and processed for leaf protein concentrates before proximate composition, mineral analysis phytochemical and antimicrobial properties were determined using a standard method of analysis. The results of proximate constituents showed; moisture content; 9.89±0.051g/100g, Ash; 3.23±0.12g/100g, crude fat; 3.96±0.11g/100g and 61.27±0.56g/100g of Nitrogen free extractive. The mineral analysis of the sample showed; Mg; 0.081±0.00mg/100g, Ca; 42.30±0.05mg/100g, Na; 27.57±0.09mg/100g, K; 6.81±0.01mg/100g, P; 8.90±0.03mg/100g, Fe; 0.51±0.00mg/100g, Zn; 0.021±0.00mg/100g, Cd; 0.04±0.04mg/100g, Pb; 0.002±0.00mg/100g, Cr; 0.041±0.00mg/100g Cadmium and Mercury were not detected in the sample. The result of phytochemical analysis of leaf protein concentrates of the Huckleberry showed the presence of Alkaloid, Saponin, Flavonoid, Tanin, Coumarin, Steroids, Terpenoids, Cardiac glycosides, Glycosides, Quinones, Anthocyanin, phytosterols, and phenols. Ethanolic extracts of the Vaccinium parvifolium L. leaf protein concentrates showed that it contains bioactive compounds that are capable of combating the following microorganisms; Staphylococcus aureus, Streptococcus pyogenes, Streptococcus faecalis, Pseudomonas aeruginosa, Klebisialae pneumonia and Proteus mirabilis. The results of the analysis of Vaccinium parvifolium L. leaf protein concentrates showed that the sample contains valuable nutrient and mineral constituents, and phytochemical compounds that could make the sample useful for medicinal activities.

Keywords: leaf protein concentrates, vaccinium parvifolium, nutritional characteristics, mineral composition, antimicrobial activity

Procedia PDF Downloads 41

Authors: Andi Aliah Hidayani, Asmi Citra Malina A. R. Tassakka, Andi Parenrengi

Abstract:

Vanname Shrimp is one of the high yielding varieties that are more resistant to virus attacks. However, now this shrimp more death due to virus attack such as white spot disease caused by white spot syndrome virus (WSSV). Various efforts have done to prevent the disease, like immunostimulatory, probiotics, and vaccine. White spot syndrome virus (WSSV) envelope protein VP19 gene is important because of its involvement in the system infection of shrimp. This study aimed to isolate and characterize an envelope protein VP19 – encoding gene of WSSV using WSSV infected Vanname Shrimp sample from some areas in South Sulawesi (Pangkep, Barru and Pinrang). The genomic of DNA were isolated from shrimp muscle using DTAB-CTAB method. Isolation of gene encoding envelope protein VP19 WSSV ws successfully performed with the results of the length of DNA fragment was 387 bp. The results of homology analysis using BLASTn homology suggested that these isolates genes from Barru, Pangkep and Pinrang have closest relationship with isolates from Mexican.

Keywords: vanname, shrimp, WSSV, viral protein 19

Procedia PDF Downloads 508

Authors: Sergio Alejandro Cuevas, Catherine Etchebest, Fernando Luis Barroso Da Silva

Abstract:

The flavivirus genus has several organisms responsible for generating various diseases in humans. Special in Brazil, Zika (ZIKV), Dengue (DENV) and Yellow Fever (YFV) viruses have raised great health concerns due to the high number of cases affecting the area during the last years. Diagnostic is still a difficult issue since the clinical symptoms are highly similar. The understanding of their common structural/dynamical and biomolecular interactions features and differences might suggest alternative strategies towards differential serological diagnostics and therapeutic intervention. Due to their immunogenicity, the primary focus of this study was on the ZIKV, DENV and YFV non-structural proteins 1 (NS1) protein. By means of computational studies, we calculated the main physical chemical properties of this protein from different strains that are directly responsible for the biomolecular interactions and, therefore, can be related to the differential infectivity of the strains. We also mapped the electrostatic differences at both the sequence and structural levels for the strains from Uganda to Brazil that could suggest possible molecular mechanisms for the increase of the virulence of ZIKV. It is interesting to note that despite the small changes in the protein sequence due to the high sequence identity among the studied strains, the electrostatic properties are strongly impacted by the pH which also impact on their biomolecular interactions with partners and, consequently, the molecular viral biology. African and Asian strains are distinguishable. Exploring the interfaces used by NS1 to self-associate in different oligomeric states, and to interact with membranes and the antibody, we could map the strategy used by the ZIKV during its evolutionary process. This indicates possible molecular mechanisms that can explain the different immunological response. By the comparison with the known antibody structure available for the West Nile virus, we demonstrated that the antibody would have difficulties to neutralize the NS1 from the Brazilian strain. The present study also opens up perspectives to computationally design high specificity antibodies.

Keywords: zika, biomolecular interactions, electrostatic interactions, molecular mechanisms

Procedia PDF Downloads 96

Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

Abstract:

Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Methicillin-resistant Staphylococcus aureus, dihydroxyacetone kinase, essential genes, drug target, phosphoryl group donor

Procedia PDF Downloads 375

Authors: Bin Liu

Abstract:

As one of the most important tasks in protein sequence analysis, protein remote homology detection has been studied for decades. Currently, the profile-based methods show state-of-the-art performance. Position-Specific Frequency Matrix (PSFM) is widely used profile. However, there exists noise information in the profiles introduced by the amino acids with low frequencies. In this study, we propose a method to remove the noise information in the PSFM by removing the amino acids with low frequencies called Top frequency profile (TFP). Three new matrix transformation methods, including Autocross covariance (ACC) transformation, Tri-gram, and K-separated bigram (KSB), are performed on these profiles to convert them into fixed length feature vectors. Combined with Support Vector Machines (SVMs), the predictors are constructed. Evaluated on two benchmark datasets, and experimental results show that these proposed methods outperform other state-of-the-art predictors.

Keywords: protein remote homology detection, protein fold recognition, top frequency profile, support vector machines

Procedia PDF Downloads 98

Authors: Nais Pinta Adetya, H. Hadiyanto

Abstract:

Microalgae has a potential to be utilized as food and natural colorant. The microalgae components consists of three main parts, these are lipid, protein, and carbohydrate. Crucial step in producing lipid and protein from microalgae is extraction. Microalgae has high water level (70-90%), it causes drying process of biomass needs much more energy and also has potential to distract lipid and protein from microalgae. Extraction of lipid from wet biomass is able to take place efficiently with cell disruption of microalgae by osmotic shock method. In this study, osmotic shock method was going to be integrated with ultrasound to maximalize the extraction yield of lipid and protein from wet biomass Spirulina sp. with osmotic shock method assisted ultrasound. This study consisted of two steps, these were osmotic shock process toward wet biomass and ultrasound extraction assisted. NaCl solution was used as osmotic agent, with the variation of concentrations were 10%, 20%, and 30%. Extraction was conducted in 40°C for 20 minutes with frequency of ultrasound wave was 40kHz. The optimal yield of protein (2.7%) and (lipid 38%) were achieved at 20% osmotic agent concentration.

Keywords: extraction, lipid, osmotic shock, protein, ultrasound

Procedia PDF Downloads 324

Authors: Olubukayo-Opeyemi Oyetayo, Oscar Mendez-Lucio, Andreas Bender, Hans Kiefer

Abstract:

The thermal melting curve of a protein provides information on its conformational stability and could provide cues on its aggregation behavior. Naturally-occurring osmolytes have been shown to improve the thermal stability of most proteins in a concentration-dependent manner. They are therefore commonly employed as additives in therapeutic protein purification and formulation. A number of intertwined and seemingly conflicting mechanisms have been put forward to explain the observed stabilizing effects, the most prominent being the preferential exclusion mechanism. We attempted to probe and summarize molecular mechanisms for thermal stabilization of a monoclonal antibody (mAb) by developing quantitative structure-activity relationships using a rationally-selected library of 120 osmolyte-like compounds in the polyhydric alcohols, amino acids and methylamines classes. Thermal stabilization potencies were experimentally determined by thermal shift assays based on differential scanning fluorimetry. The cross-validated QSAR model was developed by partial least squares regression using descriptors generated from Molecular Operating Environment software. Careful evaluation of the results with the use of variable importance in projection parameter (VIP) and regression coefficients guided the selection of the most relevant descriptors influencing mAb thermal stability. For the mAb studied and at pH 7, the thermal stabilization effects of tested compounds correlated positively with their fractional polar surface area and inversely with their fractional hydrophobic surface area. We cannot claim that the observed trends are universal for osmolyte-protein interactions because of protein-specific effects, however this approach should guide the quick selection of (de)stabilizing compounds for a protein from a chemical library. Further work with a large variety of proteins and at different pH values would help the derivation of a solid explanation as to the nature of favorable osmolyte-protein interactions for improved thermal stability. This approach may be beneficial in the design of novel protein stabilizers with optimal property values, especially when the influence of solution conditions like the pH and buffer species and the protein properties are factored in.

Keywords: thermal stability, monoclonal antibodies, quantitative structure-activity relationships, osmolytes

Procedia PDF Downloads 299

Authors: Navneet Kaur, S. D. Tiwari

Abstract:

Ferritin is a protein which present in the blood of mammals. It maintains the need of iron inside the body. It has an antiferromagnetic iron core, 7-8 nm in size, which is encapsulated inside a protein cage. The thickness of this protein shell is about 2-3 nm. This protein shell reduces the interaction among particles and make ferritin a model superparamagnet. The major composition of ferritin core is mineral ferrihydrite. The molecular formula of ferritin core is (FeOOH)8[FeOOPO3H2]. In this study, we discuss the phase transition of ferritin. We characterized ferritin using x-ray diffractometer, transmission electron micrograph, thermogravimetric analyzer and vibrating sample magnetometer. It is found that ferritin core is amorphous in nature with average particle size of 8 nm. The thermogravimetric and differential thermogravimetric analysis curves shows mass loss at different temperatures. We heated ferritin at these temperatures. It is found that ferritin core starts decomposing after 390^o C. At 1020^o C, the ferritin core is finally converted to alpha phase of iron oxide. Magnetization behavior of final sample clearly shows the iron oxyhydroxide core is completely converted to alpha iron oxide.

Keywords: Antiferromagnetic, Ferritin, Phase, Superparamagnetic

Procedia PDF Downloads 82

Authors: Caroline Picton, Lorna Moxham, Christopher Patterson, Dana Perlman, Ellie Taylor, Renee Brighton

Abstract:

The purpose of this study was to extrapolate the meaning for people living with a mental illness of their participation in a therapeutic recreation experience. The study’s participants engaged in a five-day adventure camp, known as Recovery Camp, alongside undergraduate health care students. An interpretive phenomenological approach was used as an exploratory method to interview 25 participants (n=25). Van Kaam’s structured analytical framework guided the analysis of the transcribed narratives. The findings provide insight into using therapeutic recreation to enhance personal mental health recovery. Recovery Camp was viewed by participants as having a transformational effect on forming positive social connectedness and improving their self-identity. Participants perceived the Recovery Camp experience as one that gave them a sense of purpose and increased their motivation to undertake further activities. The insights gained of the benefits of therapeutic recreation for people living with a mental illness can be used to promote purposeful community engagement.

Keywords: interpretive phenomenology, lived experience, mental illness, personal mental health recovery

Procedia PDF Downloads 466

Authors: Zarmina Gillani, Nuzhat Huma, Aysha Sameen, Mulazim Hussain Bukhari

Abstract:

Whey is an excellent food ingredient owing to its high nutritive value and its functional properties. However, composition of whey varies depending on composition of milk, processing conditions, processing method, and its whey protein content. The aim of this study was to prepare a whey powder from raw whey and to determine the influence of different processing temperatures (160 and 180 °C) on the physicochemical, functional properties during storage of 180 days and on whey protein denaturation. Results have shown that temperature significantly (P < 0.05) affects the pH, acidity, non-protein nitrogen (NPN), protein total soluble solids, fat and lactose contents. Significantly (p < 0.05) higher foaming capacity (FC), foam stability (FS), whey protein nitrogen index (WPNI), and a lower turbidity and solubility index (SI) were observed in whey powder processed at 160 °C compared to whey powder processed at 180 °C. During storage of 180 days, slow but progressive changes were noticed on the physicochemical and functional properties of whey powder. Reverse phase-HPLC analysis revealed a significant (P < 0.05) effect of temperature on whey protein contents. Denaturation of β-Lactoglobulin is followed by α-lacalbumin, casein glycomacropeptide (CMP/GMP), and bovine serum albumin (BSA).

Keywords: whey powder, temperature, denaturation, reverse phase, HPLC

Procedia PDF Downloads 270

Authors: Ana Rita Conde, Pilar Mota, Tânia Botelho, Suzana Caldeira, Isabel Rego, Jessica Pacheco, Osvaldo Silva, Áurea Sousa

Abstract:

Tourism promotes well-being and health to children with ASD and their families. Literature indicates the need to provide tourist activities that integrate the therapeutic component, to promote the development and well-being of children with ASD. The study aims to implement tourist offers in Azores that integrate the therapeutic feature, assess their suitability and impact on the well-being and health of the child and caregivers. Using a mixed methodology, the study integrates families that experience and evaluate the impact of tourism products developed specifically for them.

Keywords: austism spectrum disorder, children, therapeutic tourism activities, well-being, health, inclusive tourism

Procedia PDF Downloads 113

Authors: Dalia G. Aseel

Abstract:

The potato (Solanum tubersum, L.) has become one of the major vegetable crops in Egypt and all over the world. Potato leafroll virus(PLRV) was observed on potato plants collected from different governorates in Egypt. Three cultivars, Spunta, Diamont, and Cara, infected with PLRV were collected; RNA was extracted and subjected to Real-Time PCR using the coat protein gene primers. The results showed that the expression of the coat protein was 39.6-fold, 12.45-fold, and 47.43-fold, respectively, for Spunta, Diamont, and Cara cultivars. Differential Display Polymerase Chain Reaction (DD-PCR) using pathogenesis-related protein 1 (PR-1), β-1,3-glucanases (PR-2), chitinase (PR-3), peroxidase (POD), and polyphenol oxidase (PPO) forward primers for pathogenesis-related proteins (PR). The obtained data revealed different banding patterns depending on the viral type and the region of infection. Regarding PLRV, 58 up-regulated and 19 down-regulated genes were detected. Sequence analysis of the up-and down-regulated genes revealed that infected plants were observed in comparison with the healthy control. Sequence analysis of the up-regulated gene was performed, and the encoding sequence analysis showed that the obtained genes include: induced stolen tip protein. On the other hand, two down-regulated genes were identified: disease resistance RPP-like protein and non-specific lipid-transfer protein. In this study, the expressions of PR-1, PR-2, PR-3, POD, and PPO genes in the infected leaves of three potato cultivars were estimated by quantitative real-time PCR. We can conclude that the PLRV-infection of potato plants inhibited the expression of the five PR genes. On the contrary, infected leaves by PLRV elevated the expression of some defense genes. This interaction may also induce and/or suppress the expression of some genes responsible for the plant's defense mechanisms.

Keywords: PLRV, pathogenesis-related proteins (PRs), DD-PCR, sequence, real-time PCR

Procedia PDF Downloads 108

Authors: Hatairuk Tungkasen, Somrudee Phetchrid, Suwapat Jaidee, Supinya Yoomak, Chantana Kankamol, Mayuree Pumipaiboon, Mayuva Areekijseree

Abstract:

Ovaries of reproductive female pigs were obtained from local slaughterhouses in Nakorn Pathom Province, Thailand. Follicular fluid of medium follicle (5-6 diameters) and large follicles (7-8 mm and 10 mm in diameter) were aspirated and collected by sterile technique and analyzed protein pattern. The follicular fluid protein bands were found by SDS-PAGE which has no protein band in difference compared to standard protein band. So we chose protein band molecular weight 50, 62-65, 75-80, 90, 120-160, and >220 kDa were analyzed by LC/MS/MS. The result was found immunoglobulin gamma chain, keratin, transferrin, heat shock protein, and plasminogen precursor, ceruloplasmin, and hemopexin, and protease, respectively. All proteins play important roles in promotion and regulation on growth and development of reproductive cells. The result of this study found many proteins which were useful and important for in vitro oocyte maturation and embryonic development of cell technology in animals. The further study will be use porcine follicular fluid protein of medium and large follicles as feeder cells in in vitro condition to promote oocyte and embryo maturation.

Keywords: follicular fluid protein, LC/MS/MS, porcine oocyte, SDS-PAGE

Procedia PDF Downloads 551

Authors: Shahnaz Ashrafpour, Tahereh Tohidi Moghadam, Bijan Ranjbar

Abstract:

Identifying the nature of protein-nanoparticle interactions and favored binding sites is an important issue in functional characterization of biomolecules and their physiological responses. Herein, interaction of silver nanoparticles with lysozyme as a model protein has been monitored via fluorescence spectroscopy. Formation of complex between the biomolecule and silver nanoparticles (AgNPs) induced a steady state reduction in the fluorescence intensity of protein at different concentrations of nanoparticles. Tryptophan fluorescence quenching spectra suggested that silver nanoparticles act as a foreign quencher, approaching the protein via this residue. Analysis of the Stern-Volmer plot showed quenching constant of 3.73 µM−1. Moreover, a single binding site in lysozyme is suggested to play role during interaction with AgNPs, having low affinity of binding compared to gold nanoparticles. Unfolding studies of lysozyme showed that complex of lysozyme-AgNPs has not undergone structural perturbations compared to the bare protein. Results of this effort will pave the way for utilization of sensitive spectroscopic techniques for rational design of nanobiomaterials in biomedical applications.

Keywords: nanocarrier, nanoparticles, surface plasmon resonance, quenching fluorescence

Procedia PDF Downloads 300

Authors: Jin Boo Jeong

Abstract:

In this study, we elucidated anti-cancer activity and potential molecular mechanism of DKC against human colorectal cancer cells. DKC-E70 suppressed the proliferation of human colorectal cancer cell lines such as HCT116, SW480, LoVo and HT-29. Although DKC-E70 decreased cyclin D1 expression in protein and mRNA level, decreased level of cyclin D1 protein by DKC-E70 occurred at the earlier time than that of cyclin D1 mRNA, which indicates that DKC-E70-mediated downregulation of cyclin D1 protein may be a consequence of the induction of degradation and transcriptional inhibition of cyclin D1. In cyclin D1 degradation, we found that cyclin D1 downregulation by DKC-E70 was attenuated in presence of MG132. In addition, DKC-E70 phosphorylated threonine-286 (T286) of cyclin D1 and T286A abolished cyclin D1 downregulation by DKC-E70. We also observed that DKC-E70-mediated T286 phosphorylation and subsequent cyclin D1 degradation was blocked in presence of the inhibitors of ERK1/2, p38 or GSK3β. In cyclin D1 transcriptional inhibition, DKC-E70 inhibited the expression of β-catenin and TCF4, and β–catenin/TCF-dependent luciferase activity. Our results suggest that DKC-E70 may downregulate cyclin D1 as one of the potential anti-cancer targets through cyclin D1 degradation by T286 phosphorylation dependent on ERK1/2, p38 or GSK3β, and cyclin D1 transcriptional inhibition through Wnt signaling. From these findings, DKC-E70 has potential to be a candidate for the development of chemoprevention or therapeutic agents for human colorectal cancer. This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2016R1D1A3B03931713).

Keywords: anticancer, calyx of persimmon, cyclin D1, Diospyros kaki Thunb., human colorectal cancer

Procedia PDF Downloads 287

Authors: Hanan Azzam1, Nashwa Abousamra1, Amany Mansour1, Yaser Abd El-dayem2, , Solafa Elsharawy1

Abstract:

Background: Inherited thrombophilias are a heterogenous group of conditions which have been implicated in a variety of pregnancy complications. More recently, deficiency of protein Z (PZ) has been liked to pregnancy complications, including preterm delivery. Aim: We designed this study to evaluate the association of inherited thrombophilias including [Protein C (PC), Protein S (PS), Anti thrombin III (ATIII) deficiency and activated protein C (APC) resistance] and protein Z deficiency with a variety of pregnancy complications. Patients and Methods: 60 women with different pregnancy complications, including 20 patients with preeclampsia, 20 patients with intrauterine growth resistance (IUGR), and 20 patients with intrauterine fetal death (IUFD), in addition to 30 healthy pregnant women were recruited for the present study. PC and free PS antigen, ATIII activity, modified functional APC-resistance, and PZ levels were determined. Results: There was no significant association between inherited thrombophilias and complicated pregnancies as regards PC deficiency (p=1.0), AT III and PS deficiency (p=0.312), and APC-resistance (P=0.083). PZ was significantly associated with complicated pregnancies (p=0.012). Patients with protein Z levels below 1.5 µg/ml were considered deficient. Accordingly, we demonstrated protein Z deficiency in 30% of complicated pregnancies (RR 6.0, 95% CI 1.29-27.90;p=0.022), 20% of preeclampsia (RR 3.5, 95% CI 0.57 – 21.28; P = 0.174), 40% of IUGR (RR 9.3 95% CI 1.72-50.61; P = 0.010) and 30% of IUFD (RR 6, 95% CI 1.07 – 33.64; P = 0.042). Conclusions: These findings indicate the absence of association of inherited thrombophilias, including PC, PS, AT III deficiency, and APC resistance with pregnancy complications. However, PZ deficiency is associated with increased risk of pregnancy complications, especially intrauterine growth restriction and intrauterine fetal death.

Keywords: protein C, protein S, thrombophelia, pregnancy, protein Z

Procedia PDF Downloads 207

Authors: Hye Rim Lee, Eui Jun Jeong, Ju Woo Kim

Abstract:

This study will examine how the therapeutic factors (therapeutic catharsis-seeking and game-efficacy of the game player) and self-construal factors (independent and interdependent self-construal of the game player) as well as social capital factors (bonding and bridging social capital of the game player) affect trait aggression in the game. Results show that both therapeutic catharsis-seeking and game self-efficacy are particularly important to the players since they cause the game players’ aggressive tendencies to be greatly diminished. Independent self-construal reduces the level of the players’ aggression. Interestingly enough, the bonding social capital enhances the level of the players’ aggression, while individuals with bridging social capital did not show any significant effects. The results and implications will be discussed herein.

Keywords: aggression catharsis, game self-efficacy, self-construal, social capital, therapeutic catharsis seeking

Procedia PDF Downloads 492

Authors: Lydia Tan, Philippe Lemey, Lieselot Houspie, Marco Viveen, Darren Martin, Frank Coenjaerts

Abstract:

Introduction: Human respiratory syncytial virus (hRSV) is the leading cause of severe respiratory tract infections in infants under the age of two. Genomic substitutions and related evolutionary dynamics of hRSV are of great influence on virus transmission behavior. The evolutionary patterns formed are due to a precarious interplay between the host immune response and RSV, thereby selecting the most viable and less immunogenic strains. Studying genomic profiles can teach us which genes and consequent proteins play an important role in RSV survival and transmission dynamics. Study design: In this study, genetic diversity and evolutionary rate analysis were conducted on 36 RSV subgroup B whole genome sequences and 37 subgroup A genome sequences. Clinical RSV isolates were obtained from nasopharyngeal aspirates and swabs of children between 2 weeks and 5 years old of age. These strains, collected during epidemic seasons from 2001 to 2011 in the Netherlands and Belgium by either conventional or 454-sequencing. Sequences were analyzed for genetic diversity, recombination events, synonymous/non-synonymous substitution ratios, epistasis, and translational consequences of mutations were mapped to known 3D protein structures. We used Bayesian statistical inference to estimate the rate of RSV genome evolution and the rate of variability across the genome. Results: The A and B profiles were described in detail and compared to each other. Overall, the majority of the whole RSV genome is highly conserved among all strains. The attachment protein G was the most variable protein and its gene had, similar to the non-coding regions in RSV, more elevated (two-fold) substitution rates than other genes. In addition, the G gene has been identified as the major target for diversifying selection. Overall, less gene and protein variability was found within RSV-B compared to RSV-A and most protein variation between the subgroups was found in the F, G, SH and M2-2 proteins. For the F protein mutations and correlated amino acid changes are largely located in the F2 ligand-binding domain. The small hydrophobic phosphoprotein and nucleoprotein are the most conserved proteins. The evolutionary rates were similar in both subgroups (A: 6.47E-04, B: 7.76E-04 substitution/site/yr), but estimates of the time to the most recent common ancestor were much lower for RSV-B (B: 19, A: 46.8 yrs), indicating that there is more turnover in this subgroup. Conclusion: This study provides a detailed description of whole RSV genome mutations, the effect on translation products and the first estimate of the RSV genome evolution tempo. The immunogenic G protein seems to require high substitution rates in order to select less immunogenic strains and other conserved proteins are most likely essential to preserve RSV viability. The resulting G gene variability makes its protein a less interesting target for RSV intervention methods. The more conserved RSV F protein with less antigenic epitope shedding is, therefore, more suitable for developing therapeutic strategies or vaccines.

Keywords: drug target selection, epidemiology, respiratory syncytial virus, RSV

Procedia PDF Downloads 383

Authors: Chang Liang, Weizhi Gong, Yan Zhang

Abstract:

Purpose: Hepatocellular carcinoma (HCC) is a malignant tumor with a high mortality rate and poor prognosis worldwide. Murine double minute 2 (MDM2) regulates the tumor suppressor p53, increasing cancer risk and accelerating tumor progression. Speckle-type POX virus and zinc finger protein (SPOP), a key of subunit of Cullin-Ring E3 ligase, inhibits tumor genesis and progression by the ubiquitination of its downstream substrates. This study aimed to clarify whether SPOP and MDM2 are mutually regulated in HCC and the correlation between SPOP and MDM2 and the prognosis of HCC patients. Methods: First, the expression of SPOP and MDM2 in HCC tissues were detected by TCGA database. Then, 53 paired samples of HCC tumor and adjacent tissues were collected to evaluate the expression of SPOP and MDM2 using immunohistochemistry. Chi-square test or Fisher’s exact test were used to analyze the relationship between clinicopathological features and the expression levels of SPOP and MDM2. In addition, Kaplan‒Meier curve analysis and log-rank test were used to investigate the effects of SPOP and MDM2 on the survival of HCC patients. Last, the Multivariate Cox proportional risk regression model analyzed whether the different expression levels of SPOP and MDM2 were independent risk factors for the prognosis of HCC patients. Results: Bioinformatics analysis revealed the low expression of SPOP and high expression of MDM2 were related to worse prognosis of HCC patients. The relationship between the expression of SPOP and MDM2 and tumor stem-like features showed an opposite trend. The immunohistochemistry showed the expression of SPOP protein was significantly downregulated while MDM2 protein significantly upregulated in HCC tissue compared to that in para-cancerous tissue. Tumors with low SPOP expression were related to worse T stage and Barcelona Clinic Liver Cancer (BCLC) stage, but tumors with high MDM2 expression were related to worse T stage, M stage, and BCLC stage. Kaplan–Meier curves showed HCC patients with high SPOP expression and low MDM2 expression had better survival than those with low SPOP expression and high MDM2 expression (P < 0.05). A multivariate Cox proportional risk regression model confirmed that a high MDM2 expression level was an independent risk factor for poor prognosis in HCC patients (P <0.05). Conclusion: The expression of SPOP protein was significantly downregulated, while the expression of MDM2 significantly upregulated in HCC. The low expression of SPOP and high expression. of MDM2 were associated with malignant progression and poor prognosis of HCC patients, indicating a potential therapeutic target for HCC patients.

Keywords: hepatocellular carcinoma, murine double minute 2, speckle-type POX virus and zinc finger protein, ubiquitination

Procedia PDF Downloads 104

Authors: Alexander Hudson, Shaogang Gong

Abstract:

Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive, time-consuming analytical methods to visualise detailed protein conformation. In this study, we demonstrate that it is possible to make accurate (≥80%) predictions of protein class and architecture from structures determined at low (>3A) resolution, using a deep convolutional neural network trained on high-resolution (≤3A) structures represented as 2D matrices. Thus, we provide proof of concept for high-speed, low-cost protein structure classification at low resolution, and a basis for extension to prediction of function. We investigate the impact of the input representation on classification performance, showing that side-chain information may not be necessary for fine-grained structure predictions. Finally, we confirm that high resolution, low-resolution and NMR-determined structures inhabit a common feature space, and thus provide a theoretical foundation for boosting with single-image super-resolution.

Keywords: transfer learning, protein distance maps, protein structure classification, neural networks

Procedia PDF Downloads 105

Authors: Diana Karina Baigts Allende, Mariana Gonzalez Diaz, Luis Antonio Chel Guerrero, Mukthar Sandoval Peraza

Abstract:

Poverty and food insecurity are still incident problems in the developing countries, where population´s diet is based on cereals which are lack in protein content. Nevertheless, during last years the use of native plants has been studied as an alternative source of protein in order to improve the nutritional intake. Chaya crop also called Spinach tree, is a prehispanic plant native from Central America and South of Mexico (Mayan culture), which has been especially valued due to its high nutritional content particularly protein and some medicinal properties. The aim of this work was to study the effect of protein isolation processing from Chaya leaf harvest in Yucatan, Mexico on its structure quality in order: i) to valorize the Chaya crop and ii) to produce low-cost and high-quality protein. Chaya leaf was extruded, clarified and recovered using: a) acid precipitation by decreasing the pH value until reach the isoelectric point (3.5) and b) thermal coagulation, by heating the protein solution at 80 °C during 30 min. Solubilized protein was re-dissolved in water and spray dried. The presence of Fraction I protein, known as RuBisCO (Rubilose-1,5-biphosfate carboxylase/oxygenase) was confirmed by gel electrophoresis (SDS-PAGE) where molecular weight bands of 55 KDa and 12 KDa were observed. The infrared spectrum showed changes in protein structure due to the isolation method. The use of high temperatures (thermal coagulation) highly decreased protein solubility in comparison to isoelectric precipitated protein, the nutritional properties according to amino acid profile was also disturbed, showing minor amounts of overall essential amino acids from 435.9 to 367.8 mg/g. Chaya protein isolate obtained by acid precipitation showed higher protein quality according to essential amino acid score compared to FAO recommendations, which could represent an important sustainable source of protein for human consumption.

Keywords: chaya leaf, nutritional properties, protein isolate, protein structure

Procedia PDF Downloads 312

Authors: Alexandre Barbosa de Almeida, Telma Woerle de Lima Soares

Abstract:

Protein structure prediction is a challenging task in the bioinformatics field. The biological function of all proteins majorly relies on the shape of their three-dimensional conformational structure, but less than 1% of all known proteins in the world have their structure solved. This work proposes a deep learning model to address this problem, attempting to predict some aspects of the protein conformations. Throughout a process of multiobjective dominance, a recurrent neural network was trained to abstract the particular bias of each individual multiobjective algorithm, generating a heuristic that could be useful to predict some of the relevant aspects of the three-dimensional conformation process formation, known as protein folding.

Keywords: Ab initio heuristic modeling, multiobjective optimization, protein structure prediction, recurrent neural network

Procedia PDF Downloads 177

Authors: Ayoola, Simeon Oluwatoyin, Omogoriola Hannah Omoloye

Abstract:

The effects of 17α-Methyltestosterone Hormone on blood composition of the Sex Reversed Sarotherodon melanotheron were investigated. S. melanotheron fry were reared in six (6) plastic tanks for three (3) months, of which three (3) tanks served as treatment tanks while the other three (3) served as the control. The fry were fed with 17α-methyl testosterone enzyme, which functions as a sex reversal hormone. The fry were administered this hormone for 30 days, to ensure complete sex reversal. All the S. melanotheron fry were reared to table size for duration of three (3) months, after which, blood samples were taken from both the control and treatment fishes. The blood parameters showed no significant differences with the same values of White Blood Cell count (WBC) and Total plasma protein for the control and experimental fishes. A total protein value for sex reversed specimens was 3.99g/dL, while urea and creatinine values were 0.2g/dL. Alkaline Phosphatase, Aspartate transaminase and Alanine transaminase for the treatment specimen were 183nm/mg protein/min, 98nm/mg protein/min and 105nm/mg protein/min respectively. A total protein value for control specimens was 2.81g/dL, while urea and creatinine values were 0.2g/dL. Alkaline Phosphatase, Aspartate transaminase and Alanine transaminase for the control species were 174nm/mg protein/min, 93nm/mg protein/min and 106nm/mg protein/min respectively. The safety of MT on S. melanotheron is therefore proved since there is no adverse effect on the fish.

Keywords: 17α-Methyltestosterone, haematology, sex reversal, sarotherodon melanotheron

Procedia PDF Downloads 466

Authors: Zyrah Lou R. Samar, Genecarlo Liwanag

Abstract:

Type 2 Diabetes Mellitus is the more prevalent type, caused by a combination of insulin resistance and inadequate insulin response to hyperglycemia1. Aside from pharmacologic interventions, medical nutrition therapy is an integral part of the management of patients with Type 2 Diabetes Mellitus. Whey protein, which is one of the best protein sources, has been investigated for its applicability in improving glycemic control in patients with Type 2 Diabetes Mellitus. This systematic review and meta-analysis was conducted to measure the magnitude of the effect of whey protein on glycemic control in type 2 diabetes mellitus. The aim of this review is to evaluate the efficacy and safety of whey protein in patients with type 2 diabetes mellitus. Methods: A systematic electronic search for studies in the PubMed and Cochrane Collaboration database was done. Included in this review were randomized controlled trials of whey protein enrolling patients with type 2 diabetes mellitus. Three reviewers independently searched, assessed, and extracted data from the individual studies. Results: A systematic literature search on online databases such as Cochrane Central Registry, PubMed, and Herdin Plus was conducted in April to September 2021 to identify eligible studies. The search yielded 21 randomized controlled trials after removing duplicates. Only 5 articles were included after reviewing the full text, which met the criteria for selection. Conclusion: Whey protein supplementation significantly reduced fasting blood glucose. However, it did not reduce post-prandial blood glucose, HbA1c level, and weight when compared with the placebo. There has been a considerate heterogeneity across all studies, which may have contributed/confounded its effects. A larger sample size and better inclusion, and a more specific study may be included in the future reviews.

Keywords: whey protein, diabetes, nutrition, fasting blood sugar, postprandial glucose, HbA1c, weight reduction

Procedia PDF Downloads 78

Authors: Alise Senberga, Laila Dubova, Liene Strauta, Ina Alsina, Ieva Erdberga

Abstract:

Legume symbiotic relationship with nitrogen fixating bacteria Rhizobim leguminosarum is an important factor used to improve the productivity of legumes, due to the fact that rhizobia can supply plant with the necessary amount of nitrogen. R. leguminosarum strains have shown different activity in fixing nitrogen. Depending on the chosen R. leguminosarum strain, host plant biochemical content can be altered. In this study we focused particularly on the changes in protein content in beans (using two different varieties) and peas (five different varieties) due to the use of several different R. leguminosarum strains (four strains for both beans and peas). Overall, the protein content increase was observed after seed inoculation with R. leguminosarum. Strain and plant cultivar interaction specification was observed. The effect of R. leguminosarum inoculation on the content of protein was dependent on the R. leguminosarum strain used. Plant cultivar also appeared to have a decisive role in protein content formation with the help of R. leguminosaru.

Keywords: legumes, protein content, rhizobia strains, soil

Procedia PDF Downloads 484

Authors: Akhil Raj Pushparajan, Ranjit Ramachandran, Jijimole Gopi Reji, Ajay Kumar Ramakrishnan

Abstract:

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is one of the leading causes of death by an infectious disease. In spite of the availability of effective drugs and a vaccine, TB is a major health concern and was declared a global emergency by the World Health Organization (WHO). The success of intracellular pathogens like Mtb depends on its ability to overcome the challenging environment in the host. Gene regulation controlled by transcriptional regulators (TRs) plays a crucial role for the bacteria to adapt to the host environment. In vitro studies on gene regulatory mechanisms during dormancy and reactivation have provided insights into the adaptations employed by Mtb to survive in the host. Here we present our efforts to functionally characterize Rv1019, a putative TR of Mtb H37Rv which was found to be present at significantly varying levels during dormancy and reactivation in vitro. The expression of this protein in the dormancy-reactivation model was validated by qRT-PCR and western blot. By DNA- protein interaction studies and reporter assays we found that under normal laboratory conditions of growth this protein behaves as an auto-repressor and tetracycline was found to abrogate this repression by interfering with its ability to bind DNA. Further, by cDNA analysis, we found that this TR is co-transcribed with its downstream genes Rv1020 (mfd) and Rv1021 (mazG) which are involved in DNA damage response in Mtb. Constitutive expression of this regulator in the surrogate host M. smegmatis showed downregulation of the orthologues of downstream genes suggested that Rv1019 could negatively regulate these genes. Our finds also show that M. smegmatis expressing Rv1019 is sensitive to DNA damage suggests the role of this protein in regulating DNA damage response induced by oxidative stress. Because of its role in regulating DNA damage response which may help in the persistence of Mtb, Rv1019 could be used as a prospective target for therapeutic intervention to fight TB.

Keywords: auto-repressor, DNA repair, mycobacterium smegmatis, mycobacterium tuberculosis, tuberculosis

Procedia PDF Downloads 108

Authors: S. Kongtun-Janphuk, S. Niwitpong Jr., J. Saengsai

Abstract:

Low-sugar snack bars were formulated with 3 main formulas depending on the main ingredient, which were peanut-green bean-sesame, apple, and prune. The most acceptable formula of each group was obtained by sensory evaluation using a nine-point hedonic scale. The moisture content, total ash, protein, fat and fiber were analyzed by the standard methods of AOAC. The peanut-mung bean-sesame snack bar showed the highest protein content (88.32%) and total fat (0.48%) with the lowest of fiber content (0.01%) while the prune formula showed the lowest protein content (71.91%) and total fat (0.21%) with the highest of fiber content (0.03%). This result indicated that the prune formula could be used as diet food to assist in weight loss program.

Keywords: low-sugar snack bar, diet food, nutrition analysis, food formulation

Procedia PDF Downloads 364

Authors: Khaleel Saleh Al-Rababah

Abstract:

Amyloid fibril forming regions, which are known as protein aggregates, in sequences of some protein families are associated with a number of diseases known as amyloidosis. Mutations play a role in forming fibrils by accelerating the fibril formation process. In this paper we want to extract diseases that caused by those mutations as a result of the impact of the mutations on structural and functional properties of the aggregated protein. We propose a text mining system, to automatically extract mutations, diseases and relations between mutations and diseases. We presented an algorithm based on finite state to cluster mutations found in the same sentence as a sentence could contain different mutation cause different diseases. Also, we presented a co reference algorithm that enables cross-link sentences.

Keywords: amyloid, amyloidosis, co reference, protein, text mining

Procedia PDF Downloads 497