Search results for: genetic diversity and viral proteins

Authors: Amir Bastani

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The result of the research in the field of human behavioural genetics demonstrates a genetic contribution of behavioural differences in aggression, violence, drug and substance abuse, antisocial personality disorder and other related traits. As the field of human behavioural genetics progresses and achieves credibility, the criminal accused continue to use its types of evidence into the criminal law. One of the most important genetic factors which controls certain neurotransmitters like dopamine and serotonin is the Monoamine Oxidase Acid A (MAOA) gene, known as the 'warrior gene'. The high-profile study by Caspi and colleagues in 2002 showed that the combination between one type of variation of the MAOA gene and childhood maltreatment noticeably predisposes a person to antisocial behaviour. Moreover, further scientific research shows that individuals with the MAOA gene have to some degree difficulties in controlling their impulses. Based on the evidence of MAOA, some criminal accused claimed difficulties in self-control. In the first case – the famous case of Mobley – the court rejected the MAOA evidence on the ground of the lack of scientific support. In contrast, in other cases after the Mobley trial, courts accepted the evidence of MAOA. In this paper, the issue of lack of impulse control produced by the MAOA gene and cases which relied on the MAOA evidence and successfully being accepted will be reviewed in detail. Finally, the anticipation of the paper for the future use of the MAOA evidence in criminal cases will be presented.

Keywords: genetic defence, criminal responsibility, MAOA, self-control

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Authors: Uzma Rashid, Mommnah Asad

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As more and more people fall victim to the intolerance that has become a plague globally, academicians are faced with the herculean task of sowing the roots for more tolerant individuals. Being the multilayered task that it is, promoting an acceptance of diversity and pushing an agenda to push back hate requires efforts on multiple levels. Not only does the curriculum need to be in line with such goals, but teachers also need to be trained to cater to the sensitivities surrounding conversations of tolerance and diversity. In addition, institutional support needs to be there to provide conducive conditions for a diversity driven learning process to take place. In reality, teachers have to struggle with forwarding ideas about diversity and tolerance which do not sound particularly risky to be shared but given the current socio-political and religious milieu, can put the teacher in a difficult position and can make the task exponentially challenging. This paper is based on an auto-ethnographic account of teaching undergraduate and graduate courses at a private university in Pakistan. These courses were aimed at teaching tolerance to adult learners through classes focused on key notions pertaining to religion, culture, gender, and society. Authors’ classroom experiences with the students in these courses indicate a marked heightening of religious sensitivities that can potentially threaten a teacher’s life chances and become a hindrance in deep, meaningful conversations, thus lending a superficiality to the whole endeavor. The paper will discuss in detail the challenges that this teacher dealt with in the process, how those were addressed, and locate them in the larger picture of how tolerance can be materialized in current times in the universities in Pakistan and in similar contexts elsewhere.

Keywords: tolerance, diversity, gender, Pakistani Universities

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Authors: Kedar Nath Nepal, Tek Bahadur Thapa, David Guerena;

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The community participation is central to the in-situ project objectives, as farming communities are key stakeholders in the on-farm conservation of agricultural bio- diversity. Besides technical means to adding benefits, the complimentary strategy includes creating market-based value adding measures by increasing users’ awareness of the value of traditional foods and nutritional values; exhibitions and improved processing; and policy incentives. This paper presents various participatory activities carried out in Nepal as options for enhancing benefits to local communities by increased utilization of local crop diversity on -the farm through non-breeding discussed, and outcomes are documented using farmers’ perception data and secondary information. The paper focuses on three major areas of public awareness, market incentives and non-market incentives that may enhance on -farm conservation and use of biodiversity.

Keywords: biodiversity, in-situ, market-based, non-market

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Authors: Fouad Chebib, Marie Hogan, Ziad El-Zoghby, Maria Irazabal, Sarah Senum, Christina Heyer, Charles Madsen, Emilie Cornec-Le Gall, Atta Behfar, Barbara Ehrlich, Peter Harris, Vicente Torres

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Background: Mutations in PKD1 and PKD2, the genes encoding the proteins polycystin-1 (PC1) and polycystin-2 (PC2) cause autosomal dominant polycystic kidney disease (ADPKD). ADPKD is a systemic disease associated with several extrarenal manifestations. Animal models have suggested an important role for the polycystins in cardiovascular function. The aim of the current study is to evaluate the association of various cardiomyopathies in a large cohort of patients with ADPKD. Methods: Clinical data was retrieved from medical records for all patients with ADPKD and cardiomyopathies (n=159). Genetic analysis was performed on available DNA by direct sequencing. Results: Among the 58 patients included in this case series, 39 patients had idiopathic dilated cardiomyopathy (IDCM), 17 had hypertrophic obstructive cardiomyopathy (HOCM), and 2 had left ventricular noncompaction (LVNC). The mean age at cardiomyopathy diagnosis was 53.3, 59.9 and 53.5 years in IDCM, HOCM and LVNC patients respectively. The median left ventricular ejection fraction at initial diagnosis of IDCM was 25%. Average basal septal thickness was 19.9 mm in patients with HOCM. Genetic data was available in 19, 8 and 2 cases of IDCM, HOCM, and LVNC respectively. PKD1 mutations were detected in 47.4%, 62.5% and 100% of IDCM, HOCM and LVNC cases. PKD2 mutations were detected only in IDCM cases and were overrepresented (36.8%) relative to the expected frequency in ADPKD (~15%). The prevalence of IDCM, HOCM, and LVNC in our ADPKD clinical cohort was 1:17, 1:39 and 1:333 respectively. When compared to the general population, IDCM and HOCM was approximately 10-fold more prevalent in patients with ADPKD. Conclusions: In summary, we suggest that PKD1 or PKD2 mutations may predispose to idiopathic dilated or hypertrophic cardiomyopathy. There is a trend for patients with PKD2 mutations to develop the former and for patients with PKD1 mutations to develop the latter. Predisposition to various cardiomyopathies may be another extrarenal manifestation of ADPKD.

Keywords: autosomal dominant polycystic kidney (ADPKD), polycystic kidney disease, cardiovascular, cardiomyopathy, idiopathic dilated cardiomyopathy, hypertrophic cardiomyopathy, left ventricular noncompaction

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Authors: Joseph F. Cabrera, Rachael Dela Cruz

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This study specifically examines patterns that define ethnoracially diverse neighborhoods. Ethnoracial diversity is important as it facilitates cross-racial interactions within neighborhoods which have been theorized to be associated with such outcomes as intergroup harmony, the reduction of racial and ethnic prejudice and discrimination, and increases in racial tolerance. Los Angeles (LA) is an ideal location to study ethnoracial spatial patterns as it is one of the most ethnoracially diverse cities in the world. A large influx of Latinos, as well as Asians, have contributed to LA’s urban landscape becoming increasingly diverse over several decades. Our dataset contains all census tracts in Los Angeles County in 2016 and incorporates Census and ACS demographic and spatial data. We quantify ethnoracial diversity using a derivative of Simpson’s Diversity Index and utilize this measure to test previous literature that suggests Latinos are one of the key drivers of changing ethnoracial spatial patterns in Los Angeles. Preliminary results suggest that there has been an overall increase in ethnoracial diversity in Los Angeles neighborhoods over the past sixteen years. Patterns associated with this trend include decreases in predominantly white and black neighborhoods, increases in predominantly Latino and Asian neighborhoods, and a general decrease in the white populations of the most diverse neighborhoods. A similar pattern is seen in neighborhoods with large Latino increases- a decrease in white population, but with an increase in Asian and black populations. We also found support for previous research that suggests increases in Latino and Asian populations act as a buffer, allowing for black population increases without a sizeable decrease in the white population. Future research is needed to understand the underlying causes involved in many of the patterns and trends highlighted in this study.

Keywords: race, race and interaction, racial harmony, social interaction

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Authors: M. Sakthivel, A. Devaki, D. Balasubramanyam, P. Kumarasamy, A. Raja, R. Anilkumar, H. Gopi

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The New Zealand White breed of rabbit is one of the most commonly used, well adapted exotic breeds in India. Earlier studies were limited only to analyze the environmental factors affecting the growth and reproductive performance. In the present study, the population of the New Zealand White rabbits in a closed herd was evaluated for its genetic structure. Data on pedigree information (n=2508) for 18 years (1995-2012) were utilized for the study. Pedigree analysis and the estimates of population genetic parameters based on gene origin probabilities were performed using the software program ENDOG (version 4.8). The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.489 years, 13.233 percent and 17.585 percent, respectively. The proportion of population inbred was 100 percent. The estimated mean values of average relatedness and the individual increase in inbreeding were 22.727 and 3.004 percent, respectively. The percent increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations, and complete generations, respectively. The number of ancestors contributing the most of 50% genes (fₐ₅₀) to the gene pool of reference population was 4 which might have led to the reduction in genetic variability and increased amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (fₑ) and the effective number of ancestors (fₐ), as expressed by the fₑ/fₐ ratio was 1.1 which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29 percent pedigree was complete reflecting the well-maintained pedigree records. The maximum known generations were 15 with an average of 7.9 and the average equivalent generations traced were 5.6 indicating of a fairly good depth in pedigree. The realized effective population size was 14.93 which is very critical, and with the increasing trend of inbreeding, the situation has been assessed to be worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10 percent which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred with very high inbreeding coefficient and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve the genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.

Keywords: effective population size, genetic structure, pedigree analysis, rabbit genetics

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Authors: Yezli-Touiker Samira, Amrani-Kirane Leila, Soltani Mazouni Nadia

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Due to secondary effects of conventional insecticides on the environment, the agrochemical research has resulted in the discovery of novel molecules. That research work will help in the development of a new group of pesticides that may be cheaper and less hazardous to the environment and non-target organisms which is the main desired outcome of the present work. Angiotensin-converting enzyme as a target for the development of novel insect growth regulators. Captopril is an inhibitor of angiotensin converting enzyme (ACE) it was tested in vivo by topical application on reproduction of Ephestia kuehniella Zeller (Lepidoptera: Pyralidae). The compound is diluted in acetone and applied topically to newly emerged pupae (10µg/ 2µl). The effects of this molecule was studied,on the biochemistry of ovary (on amounts nucleic acid, proteins, the qualitative analysis of the ovarian proteins and the reproductive potential (duration of the pre-oviposition, duration of the oviposition, number of eggs laid and hatching percentage). Captopril reduces significantly quantity of ovarian proteins and nucleic acid. The electrophoresis profile reveals the absence of tree bands at the treated series. This molecule reduced the duration of the oviposition period, the fecundity and the eggviability.

Keywords: environment, ephestia kuehniella, captopril, reproduction, the agrochemical research

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Authors: Marta Fernández Olmos, Ana Gargallo Castel, Alice Salami

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The literature has shown the importance of studying the issue of business survival in highly competitive environments. In particular, the wine sector has certain characteristics that make it interesting to study factors that increase the possibility of wineries' survival, such as individual productivity, winery size, age, innovation efforts or the maturity of the industry itself, among others. Due to the importance of these factors, this research aims to analyze whether the possibility of wineries' survival increases if they are family businesses or if there is gender diversity in senior management. To this end, a nationwide survey was carried out. The sample was made up of wineries from all the Spanish appellations of origin, using this sample to analyze the survival of the diverse types of wineries according to the factors to be studied. The main results indicate that family wineries survive longer, suggesting that this may be due to the fact that the main objective of family wineries is the continuity of the business in the long term. Regarding gender diversity, wineries that have a female presence in top roles in management, adding gender diversity, survive more than those with a predominantly male presence. Based on these results, it is advisable to consider the importance of family businesses, especially in this type of sector. In addition, support should be provided for the inclusion of a female labor force to improve the possibility of survival.

Keywords: gender, family business, wine industry, survival

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Authors: Abu Salim Mustafa

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The comparisons of mycobacterial genomes have identified several Mycobacterium tuberculosis-specific genomic regions that are absent in other mycobacteria and are known as regions of differences. Due to M. tuberculosis-specificity, the peptides encoded by these regions could be useful in the specific diagnosis of tuberculosis. To explore this possibility, overlapping synthetic peptides corresponding to 39 proteins predicted to be encoded by genes present in regions of differences were tested for antibody-reactivity with sera from tuberculosis patients and healthy subjects. The results identified four immunodominant peptides corresponding to four different proteins, with three of the peptides showing significantly stronger antibody reactivity and rate of positivity with sera from tuberculosis patients than healthy subjects. The fourth peptide was recognized equally well by the sera of tuberculosis patients as well as healthy subjects. Predication of antibody epitopes by bioinformatics analyses using ABCpred server predicted multiple linear epitopes in each peptide. Furthermore, peptide sequence analysis for sequence identity using BLAST suggested M. tuberculosis-specificity for the three peptides that had preferential reactivity with sera from tuberculosis patients, but the peptide with equal reactivity with sera of TB patients and healthy subjects showed significant identity with sequences present in nob-tuberculous mycobacteria. The three identified M. tuberculosis-specific immunodominant peptides may be useful in the serological diagnosis of tuberculosis.

Keywords: genomic regions of differences, Mycobacterium tuberculossis, peptides, serodiagnosis

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Authors: Saloni Diwakar, Hansika Kapoor

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The study undertook comparative analyses between 130 male and female managers in a power/electric company, relating to prevalent perceptions about gendered leadership, leadership efficacy, perceived organizational support, and diversity and inclusiveness. Results showed no significant difference in POS, leadership aspirations, expression, and self- and other leadership efficacy between male and female managers. However, within-groups analyses revealed that female managers reported a disparity between self and other leadership efficacy (value), to a far greater extent than male managers (value). Additionally, females reported a dip in POS during middle management, as compared to junior management, whereas men reported a steady increase in POS from junior, middle on to senior management. Descriptively, both men and women reported preferring gender neutral leadership traits, as compared to male or female centered traits, and both genders least preferred male centered leadership traits. Compared to women, male managers were found to significantly undervalue diversity and inclusion initiatives. Subjective feedback was elicited to corroborate quantitative output. Also, female participants provided subjective feedback regarding efficacy of existing D&I practices in the organization. Findings and implications are discussed relevant to existing gender inclusion agendas.

Keywords: gendered leadership, diversity, inclusivity, perceived organizational support

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Authors: D. L. David, J. A. Wahedi, Q. T. Zaku

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A study was conducted at River Mayo Ranewo and River Lau, Taraba State Nigeria. The two rivers empty into the Upper Benue Basin. A visual encounter survey was conducted within the two wetlands from June to August, 2014. The fish record was based entirely on landings of fishermen, number of canoes that land fish was counted, types of nets and baits used on each sampling day. Fish were sorted into taxonomic groups, identified to family/species level, counted and weighed in groups. The relative species abundance was determined by dividing the number of species from a site by the total number of species from all tributaries/sites. Fish was preserved in 2% formaldehyde solution and taken to the laboratory, where they were identified. Shannon-Weiner index of species diversity indicated that the diversity was highest at River Mayo Ranewo than River Lau. In the result showed at River Mayo Ranewo, the family Mochokidae recorded the highest (23.15%), followed by Mormyridae (2.64%) and the least was the family Lepidosirenidae (0.04%). While at River Lau the family Mochokidae recorded the highest occurrence of (24.1%), followed by Bagridae (20.20%), and then Mormyridae, which also was the second highest in River Lau, with 18.46% occurrence. There was no occurrence of Malapteruridae and Osteoglossidae (0%) in River Lau, but the least occurrence was the family Gymnarchidae (0.04%). These results indicated that the fish composition were not significantly (p ≤ 0.05) different based on t-test.

Keywords: conservation, diversity index, Lau, Mayo Ranewo, wetlands

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Authors: Soo Dong Cho, In-Ohk Ouh, Byeong Sul Kang, Seyeon Park, In-Soo Cho, Jae Young Song

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An VP2 gene from the current prevalent CPV (Canine Parvovirus) strain (new CPV-2a) in the Republic of Korea was expressed in a baculovirus expression system. Genomic DNA was extracted from the isolate strain CPV-2a. The recombinant baculovirus, containing the coding sequences of VP2 with the histidine tag at the N-terminus, were generated by using the Bac-to-Bac system. For production of the recombinant VP2 proteins, SF9 cells were transfection into 6 wells. Propagation of recombinant baculoviruses and expression of the VP2 protein were performed in the Sf9 cell line maintained. The proteins were detected to Western blot anlaysis. CPV-2a VP2 was detected by Western blotting the monoclonal antibodies recognized 6x His and the band had a molecular weight of 65 KDa. We demonstrated that recombinant CPV-2a VP2 expression in baculovirus. The recombinant CPV-2a VP2 may able to development of specific diagnostic test and vaccination of against CPV2. This study provides a foundation for application of CPV2 on the development of new CPV2 subunit vaccine.

Keywords: baculovirus, canine parvovirus 2a, Dog, Korea

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Authors: Pedro M. Rodrigues, Claudia Raposo, Denise Schrama, Marco Cerqueira

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Farmed fish welfare is a very recent concept, widely discussed among the scientific community. Consumers’ interest regarding farmed animal welfare standards has significantly increased in the last years posing a huge challenge to producers in order to maintain an equilibrium between good welfare principles and productivity, while simultaneously achieve public acceptance. The major bottleneck of standard aquaculture is to impair considerably fish welfare throughout the production cycle and with this, the quality of fish protein. Welfare assessment in farmed fish is undertaken through the evaluation of fish stress responses. Primary and secondary stress responses include release of cortisol and glucose and lactate to the blood stream, respectively, which are currently the most commonly used indicators of stress exposure. However, the reliability of these indicators is highly dubious, due to a high variability of fish responses to an acute stress and the adaptation of the animal to a repetitive chronic stress. Our objective is to use comparative proteomics to identify and validate a fingerprint of proteins that can present an more reliable alternative to the already established welfare indicators. In this way, the culture conditions will improve and there will be a higher perception of mechanisms and metabolic pathway involved in the produced organism’s welfare. Due to its high economical importance in Portuguese aquaculture Gilthead seabream will be the elected species for this study. Protein extracts from Gilthead Seabream fish muscle, liver and plasma, reared for a 3 month period under optimized culture conditions (control) and induced stress conditions (Handling, high densities, and Hipoxia) are collected and used to identify a putative fish welfare protein markers fingerprint using a proteomics approach. Three tanks per condition and 3 biological replicates per tank are used for each analisys. Briefly, proteins from target tissue/fluid are extracted using standard established protocols. Protein extracts are then separated using 2D-DIGE (Difference gel electrophoresis). Proteins differentially expressed between control and induced stress conditions will be identified by mass spectrometry (LC-Ms/Ms) using NCBInr (taxonomic level - Actinopterygii) databank and Mascot search engine. The statistical analysis is performed using the R software environment, having used a one-tailed Mann-Whitney U-test (p < 0.05) to assess which proteins were differentially expressed in a statistically significant way. Validation of these proteins will be done by comparison of the RT-qPCR (Quantitative reverse transcription polymerase chain reaction) expressed genes pattern with the proteomic profile. Cortisol, glucose, and lactate are also measured in order to confirm or refute the reliability of these indicators. The identified liver proteins under handling and high densities induced stress conditions are responsible and involved in several metabolic pathways like primary metabolism (i.e. glycolysis, gluconeogenesis), ammonia metabolism, cytoskeleton proteins, signalizing proteins, lipid transport. Validition of these proteins as well as identical analysis in muscle and plasma are underway. Proteomics is a promising high-throughput technique that can be successfully applied to identify putative welfare protein biomarkers in farmed fish.

Keywords: aquaculture, fish welfare, proteomics, welfare biomarkers

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Authors: Nafees Ahmed, Nur Izyani Kamaruzman, Saralla Nathan, Mohd Ezharul Hoque Chowdhury, Anuar Zaini Md Zain, Iekhsan Othman, Sharifah Binti Syed Hassan

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Meat quality is always subject to consumer scrutiny when purchasing from retail markets on mislabeling as fresh meat. Various physiological and biochemical changes influence the quality of meat. As a major component of muscle tissue, proteins play a major role in muscle foods. In meat industry, freezing is the most common form of storage of meat products. Repeated cycles of freezing and thawing are common in restaurants, kitchen, and retail outlets and can also occur during transportation or storage. Temperature fluctuation is responsible for physical, chemical, and biochemical changes. Repeated cycles of ‘freeze-thaw’ degrade the quality of meat by stimulating the lipid oxidation and surface discoloration. The shelf life of meat is usually determined by its appearance, texture, color, flavor, microbial activity, and nutritive value and is influenced by frozen storage and subsequent thawing. The main deterioration of frozen meat during storage is due to protein. Due to the large price differences between fresh and frozen–thawed meat, it is of great interest to consumer to know whether a meat product is truly fresh or not. Researchers have mainly focused on the reduction of moisture loss due to freezing and thawing cycles of meat. The water holding capacity (WHC) of muscle proteins and reduced water content are key quality parameters of meat that ultimately changes color and texture. However, there has been limited progress towards understanding the actual mechanisms behind the meat quality changes under the freeze–thaw cycles. Furthermore, effect of freeze-thaw process on integrity of proteins is ignored. In this paper, we have studied the effect of ‘freeze-thawing’ on physicochemical changes of chicken meat protein. We have assessed the quality of meat by pH, spectroscopic measurements, Western Blot. Our results showed that increase in freeze-thaw cycles causes changes in pH. Measurements of absorbance (UV-visible and IR) indicated the degradation of proteins. The expression of various proteins (CREB, AKT, MAPK, GAPDH, and phosphorylated forms) were performed using Western Blot. These results indicated the repeated cycles of freeze-thaw is responsible for deterioration of protein, thus causing decrease in nutritious value of meat. It damges the use of these products in Islamic Sharia.

Keywords: chicken meat, freeze-thaw, halal, protein, western blot

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Authors: María José Bugueño, Natalia Jaime, Cristian Castro, Diego Naranjo, Guido Trautmann, Mario Pérez-Won, Vilbett Briones-Labarca

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Proteins play a crucial role in various prepared foods, including dairy products, drinks, emulsions, and ready meals. These food proteins are naturally present in food waste and byproducts. The alkaline extraction and acid precipitation method is commonly used to extract proteins from plants and animals due to its product stability, cost-effectiveness, and ease of use. This study aimed to investigate the impact of pH-shifting storage at two different pH levels on the conformational changes affecting the physicochemical and functional properties of quinoa protein isolate (QPI) and yellow shrimp byproduct protein isolate (YSPI). The QPI and YSPI were extracted using the alkaline extraction-isoelectric precipitation method. The dispersions were adjusted to pH 4 or 12, stirred for 2 hours at 20°C to achieve a uniform dispersion, and then freeze-dried. Various analyses were conducted, including flexibility (F), free sulfhydryl content (Ho), emulsifying activity (EA), emulsifying capacity (EC), water holding capacity (WHC), oil holding capacity (OHC), intrinsic fluorescence, ultraviolet spectroscopy, differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR) to assess the properties of the protein isolates. pH-shifting at pH 11 and 12 for QPI and YSPI, respectively, significantly improved protein properties, while property modification of the samples treated under acidic conditions was less pronounced. Additionally, the pH 11 and 12 treatments significantly improved F, Ho, EA, WHC, OHC, intrinsic fluorescence, ultraviolet spectroscopy, DSC, and FTIR. The increase in Ho was due to disulfide bond disruption, which produced more protein sub-units than other treatments for both proteins. This study provides theoretical support for comprehensively elucidating the functional properties of protein isolates, promoting the application of plant proteins and marine byproducts. The pH-shifting process effectively improves the emulsifying property and stability of QPI and YSPI, which can be considered potential plant-based or marine byproduct-based emulsifiers for use in the food industry.

Keywords: quinoa protein, yellow shrimp by-product protein, physicochemical properties, structural properties

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Authors: Yasser M. Saad, Heba El-Sebaie Abd El-Sadek

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Some Metapenaeus monoceros cox1 gene fragments were isolated, purified, sequenced, and comparatively analyzed with some other Crustacean Cox1 gene sequences (obtained from National Center for Biotechnology Information). This work was designed for testing the efficiency of this system in reconstruction of phylogenetic relations among some Crustacean species belonging to four genera (Metapenaeus, Artemia, Daphnia and Calanus). The single nucleotide polymorphism and haplotype diversity were calculated for all estimated mt-DNA fragments. The genetic distance values were 0.292, 0.015, 0.151, and 0.09 within Metapenaeus species, Calanus species, Artemia species, and Daphnia species, respectively. The reconstructed phylogenetic tree is clustered into some unique clades. Cytochrome oxidase subunit 1 gene (cox1) was a powerful system in reconstruction of phylogenetic relations among evaluated crustacean species.

Keywords: crustaceans, genetics, Cox1, phylogeny

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Authors: Rouhallah Bagheri, Morteza Mahmoudi, Hadi Moheb-Alizadeh

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In this paper, we develop a supplier selection and order allocation multi-objective model in stochastic environment in which purchasing cost, percentage of delivered items with delay and percentage of rejected items provided by each supplier are supposed to be stochastic parameters following any arbitrary probability distribution. To do so, we use dependent chance programming (DCP) that maximizes probability of the event that total purchasing cost, total delivered items with delay and total rejected items are less than or equal to pre-determined values given by decision maker. After transforming the above mentioned stochastic multi-objective programming problem into a stochastic single objective problem using minimum deviation method, we apply a genetic algorithm to get the later single objective problem solved. The employed genetic algorithm performs a simulation process in order to calculate the stochastic objective function as its fitness function. At the end, we explore the impact of stochastic parameters on the given solution via a sensitivity analysis exploiting coefficient of variation. The results show that as stochastic parameters have greater coefficients of variation, the value of objective function in the stochastic single objective programming problem is worsened.

Keywords: dependent chance programming, genetic algorithm, minimum deviation method, order allocation, supplier selection

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Authors: Mohit Wadhawan, Sushma Rathaur

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Lymphatic filariasis, also called elephantiasis is a tropical disease afflicting over 120 million people in 81 countries worldwide. Existing anti filarial drugs are effective against the larval stages of filarial parasites which call for an urgent need of drugs which are macrofilaricidal. Identification of molecular targets crucial for survival of filarial parasites is a prerequisite for drug designing. Prolyl oligopeptidase (POP) is one such crucial enzyme involved in the maturation and degradation of neuropeptides and peptide hormones. We have identified this peptidase in the bovine filarial parasite, Setaria cervi. Effect of inhibition of POP on the proteome profile of filarial parasite has been discussed in this study. Filarial parasites were exposed to Z-pro-prolinal (ZPP), a specific POP inhibitor for 8 h and the motility and viability of the parasites was observed. It significantly reduced the motility and viability of the parasites. To study the proteome profile, the cytosolic, endoplasmic reticulum (ER) and mitochondrial extracts of the adult female parasites were subjected to 2-dimensional electrophoresis. As analyzed by the PD-Quest software, the ZPP caused the alteration in the different subcellular proteins, and the significantly altered proteins were identified using MALDI-MS/MS spectrometry. The major proteins identified were found to play important role in diverse biological functions like signaling, redox regulation, energy metabolism, stress response, and cytoskeleton formation. Moreover, we found upregulation in the calcium binding proteins such as calreticulin, calponin, and calpain-6 suggesting that POP inhibition regulates calcium release. This relates to earlier reports that POP plays non-catalytic role in inositol 1,4,5-trisphosphate (IP3) signaling inducing release of calcium from ER. Taken together, the data demonstrated that inhibition of prolyl oligopeptidase alter the overall proteome signifying its role in survival of the filarial parasites. Thus this study provides a basis for the use of POP as a chemotherapeutic target for the treatment of lymphatic filariasis.

Keywords: lymphatic filariasis, setaria cervi, prolyl oligopeptidase, proteomics

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Authors: Essa Abrahim Abdulgader Saleem, Thien-My Dao

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The main objective of this paper is to optimize series-parallel system reliability using Genetic Algorithm (GA) and statistical analysis; considering system reliability constraints which involve the redundant numbers of selected components, total cost, and total weight. To perform this work, firstly the mathematical model which maximizes system reliability subject to maximum system cost and maximum system weight constraints is presented; secondly, a statistical analysis is used to optimize GA parameters, and thirdly GA is used to optimize series-parallel systems reliability. The objective is to determine the strategy choosing the redundancy level for each subsystem to maximize the overall system reliability subject to total cost and total weight constraints. Finally, the series-parallel system case study reliability optimization results are showed, and comparisons with the other previous results are presented to demonstrate the performance of our GA.

Keywords: reliability, optimization, meta-heuristic, genetic algorithm, redundancy

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Authors: E. Tandis, E. Assareh

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Designing the optimal shape of MW wind turbine blades is provided in a number of cases through evolutionary algorithms associated with mathematical modeling (Blade Element Momentum Theory). Evolutionary algorithms, among the optimization methods, enjoy many advantages, particularly in stability. However, they usually need a large number of function evaluations. Since there are a large number of local extremes, the optimization method has to find the global extreme accurately. The present paper introduces a new population-based hybrid algorithm called Genetic-Based Bees Algorithm (GBBA). This algorithm is meant to design the optimal shape for MW wind turbine blades. The current method employs crossover and neighborhood searching operators taken from the respective Genetic Algorithm (GA) and Bees Algorithm (BA) to provide a method with good performance in accuracy and speed convergence. Different blade designs, twenty-one to be exact, were considered based on the chord length, twist angle and tip speed ratio using GA results. They were compared with BA and GBBA optimum design results targeting the power coefficient and solidity. The results suggest that the final shape, obtained by the proposed hybrid algorithm, performs better compared to either BA or GA. Furthermore, the accuracy and speed convergence increases when the GBBA is employed

Keywords: Blade Design, Optimization, Genetic Algorithm, Bees Algorithm, Genetic-Based Bees Algorithm, Large Wind Turbine

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Authors: Alireza Dantism

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Presently, describing the function of a protein sequence is one of the most common problems in biology. Usually, this problem can be facilitated by studying the three-dimensional structure of proteins. In the absence of a protein structure, comparative modeling often provides a useful three-dimensional model of the protein that is dependent on at least one known protein structure. Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) mainly based on its alignment with one or more proteins of known structure (templates). Comparative modeling consists of four main steps 1. Similarity between the target sequence and at least one known template structure 2. Alignment of target sequence and template(s) 3. Build a model based on alignment with the selected template(s). 4. Prediction of model errors 5. Optimization of the built model There are many computer programs and web servers that automate the comparative modeling process. One of the most important advantages of these servers is that it makes comparative modeling available to both experts and non-experts, and they can easily do their own modeling without the need for programming knowledge, but some other experts prefer using programming knowledge and do their modeling manually because by doing this they can maximize the accuracy of their modeling. In this study, a web-based tool has been designed to predict the tertiary structure of proteins using PHP and Python programming languages. This tool is called EasyModel. EasyModel can receive, according to the user's inputs, the desired unknown sequence (which we know as the target) in this study, the protein sequence file (template), etc., which also has a percentage of similarity with the primary sequence, and its third structure Predict the unknown sequence and present the results in the form of graphs and constructed protein files.

Keywords: structural bioinformatics, protein tertiary structure prediction, modeling, comparative modeling, modeller

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Authors: Morteza Azimi

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In Afghanistan, as a multi-ethnic country, there have been ethnic conflicts, especially after 2001. These conflicts are more visible among the four main ethnicities Pashtun, Tajik, Hazara, and Uzbek. In this paper, such ethnic conflicts and their roles in the political sphere will be discussed. The distribution of personal electronic ID cards, for example, has been one of the most controversial and unsuccessful projects in Afghanistan. As a result, the lack of clear population statistics has led to several corrupted and unsuccessful presidential elections since 2001. The nation-building process in post-Taliban Afghanistan, as well as the Afghan government’s failure to build a nation, are discussed. By referring to the hybridity theory of Homi Bhabha, it is argued that the process of assimilation for nation-building has not only failed but has deepened ethnic divisions. In the end, some suggestions and solutions for making the most out of ethnic diversity rather than suffering from it will be provided. It will be argued that diversity or difference improves the freedom of choices for groups and individuals; it boosts agency in comparison with life in an assimilated, coherent, and homogeneous society.

Keywords: Afghan identity, ethnicity, nation-building, political system, self and other

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Authors: Niv Papo

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Characterizing the binding selectivity landscape of interacting proteins is crucial both for elucidating the underlying mechanisms of their interaction and for developing selective inhibitors. However, current mapping methods are laborious and cannot provide a sufficiently comprehensive description of the landscape. Here, we introduce a distinct and efficient strategy for comprehensively mapping the binding landscape of proteins using a combination of experimental multi-target selective library screening and in silico next-generation sequencing analysis. We map the binding landscape of a non-selective trypsin inhibitor, the amyloid protein precursor inhibitor (APPI), to each of four human serine proteases (kallikrein-6, mesotrypsin, and anionic and cationic trypsins). We then use this map to dissect and improve the affinity and selectivity of APPI variants toward each of the four proteases. Our strategy can be used as a platform for the development of a new generation of target-selective probes and therapeutic agents based on selective protein–protein interactions.

Keywords: drug design, directed evolution, protein engineering, protease inhibition.

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Authors: Hyungoo Kang, Jinkoo Kim

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This study investigated the determination of the optimal location and friction force of friction dampers to effectively reduce the seismic response of a reinforced concrete structure designed without considering seismic load. To this end, the genetic algorithm process was applied and the results were compared with those obtained by simplified methods such as distribution of dampers based on the story shear or the inter-story drift ratio. The seismic performance of the model structure with optimally positioned friction dampers was evaluated by nonlinear static and dynamic analyses. The analysis results showed that compared with the system without friction dampers, the maximum roof displacement and the inter-story drift ratio were reduced by about 30% and 40%, respectively. After installation of the dampers about 70% of the earthquake input energy was dissipated by the dampers and the energy dissipated in the structural elements was reduced by about 50%. In comparison with the simplified methods of installation, the genetic algorithm provided more efficient solutions for seismic retrofit of the model structure.

Keywords: friction dampers, genetic algorithm, optimal design, RC buildings

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Authors: Javier Enciso-Benavides, Fredy Fabian, Carlos Castaneda, Luis Alfaro, Alex Choque, Aparicio Aguilar, Javier Enciso

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Background: The use of biomarkers in breast cancer diagnosis, therapy, and prognosis has gained increasing interest. Cancer stem cells (CSCs) are a subpopulation of tumor cells that can drive tumor initiation and may cause relapse. Therefore, due to the importance of diagnosis, therapy, and prognosis, several biomarkers that characterize CSCs have been identified; however, in treatment-naïve triple-negative breast tumors, there is an urgent need to identify new biomarkers and therapeutic targets. According to this, the aim of this study was to identify serum proteins associated with cancer stem cells and pluripotency in women with triple-negative breast tumors in order to subsequently identify a biomarker for this type of breast tumor. Material and Methods: Whole blood samples from 12 women with histopathologically diagnosed triple-negative breast tumors were used after obtaining informed consent from the patient. Blood serum was obtained by conventional procedure and frozen at -80ºC. Identification of cancer stem cell-associated proteins was performed by matrix-assisted laser desorption/ionisation-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS), protein analysis was obtained using the AB Sciex TOF/TOF™ 5800 system (AB Sciex, USA). Sequences not aligned by ProteinPilot™ software were analyzed by Protein BLAST. Results: The following proteins related to pluripotency and cancer stem cells were identified by MALDI TOF/TOF mass spectrometry: A-chain, Serpin A12 [Homo sapiens], AIEBP [Homo sapiens], Alpha-one antitrypsin, AT {internal fragment} [human, partial peptide, 20 aa] [Homo sapiens], collagen alpha 1 chain precursor variant [Homo sapiens], retinoblastoma-associated protein variant [Homo sapiens], insulin receptor, CRA_c isoform [Homo sapiens], Hydroxyisourate hydrolase [Streptomyces scopuliridis], MUCIN-6 [Macaca mulatta], Alpha-actinin-3 [Chrysochloris asiatica], Polyprotein M, CRA_d isoform, partial [Homo sapiens], Transcription factor SOX-12 [Homo sapiens]. Recommendations: The serum proteins identified in this study should be investigated in the exosome of triple-negative breast cancer stem cells and in the blood serum of women without breast cancer. Subsequently, proteins found only in the blood serum of women with triple-negative breast cancer should be identified in situ in triple-negative breast cancer tissue in order to identify a biomarker to study the evolution of this type of cancer, or that could be a therapeutic target. Conclusions: Eleven cancer stem cell-related serum proteins were identified in 12 women with triple-negative breast cancer, of which MUCIN-6, retinoblastoma-associated protein variant, transcription factor SOX-12, and collagen alpha 1 chain are the most representative and have not been studied so far in this type of breast tumor. Acknowledgement: This work was supported by Proyecto CONCYTEC–Banco Mundial “Mejoramiento y Ampliacion de los Servicios del Sistema Nacional de Ciencia Tecnología e Innovacion Tecnologica” 8682-PE (104-2018-FONDECYT-BM-IADT-AV).

Keywords: triple-negative breast cancer, MALDI TOF/TOF MS, serum proteins, cancer stem cells

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Authors: Takele Bekele Bayu

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Though Ethiopia is an ancient country with ethnocultural and linguistic diversity, modern Ethiopia came into being in the second half of the 19th century under the military expansion of King Menelik II. Since then, the subsequent political system in the country failed to recognize and accommodate the country’s ethnolinguistic diversity. However, in 1991 the new government led by the Ethiopian People's Revolutionary Democratic Front (EPRDF) adopted federal-state structuring whereby constitutionally recognized and institutionally accommodated the country’s diversity. This investigation aimed to analyze drivers of ethnic conflict and its dynamism along the Eastern shared border of the Somali and Oromia regional administrations within the federal framework. The paper employed a comparative research design, adopted mixed research methods, and used survey questionnaires and focus group discussions (FGDs) for data collection. The study found that the Somali-Oromo conflict is complex and the dynamics and the sources of conflict in the study areas are similar.

Keywords: Ethiopia, Oromo, Somali, ethnic conflict, federalism

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Authors: Nina Berding

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Migration and the ensuing diversity are integral parts of urban societies. However, engaging with the urban society and its diversification is rarely perceived as something trivial but rather as a difficult task and a major challenge. A central aspect of the discourse is the current migration of refugees from countries of the southern hemisphere to Europe and the resulting challenges for cities, their municipalities and the civil society as a whole. Based on exploratory field research in a German inner-city neighborhood, it is aimed to show that the discourses about migration and diversity are completely contrary to the everyday life actions of the urban society. Processes of migration that include leaving one’s hometown and moving to other places, searching for ‘safe’ environments or better opportunities are, historically speaking, not a new phenomenon. The urban dwellers have a large repertoire of strategies in managing processes of difference in everyday life situations, guided them well for centuries and also in these contemporary processes with an increased mobility and diversity. So there is obviously a considerable discrepancy between what is practically lived in everyday life, and how it is talked about. The results of the study demonstrate that the current discourse about the challenges of migration seems to legitimize interventions beyond humanist approaches where migrants serve as collective scapegoats for social problems and affected by different discrimination and criminalization processes. On the one hand, everyone takes advantage of the super-mobility and super-diversity in their daily lives and on the other hand, powerful stakeholders and designated authorities operate a sort of retro- nationalism and identity collectivism. Political players, the municipalities and other stakeholders then follow an urban public policy that takes actions (increasing police presence, concepts and activities for special groups, exclusion from active social life, preventing participation etc.) towards different ‘groups’ of residents, produced along ‘ethnic’ lines. The results also show that, despite the obstacles and adversities placed in their way, the excluded residents perpetually relocate and re-position themselves and attempt to empower themselves by redefining their identities in their neighborhood.

Keywords: coexistence, everyday life, migration and diversity regimes, urban policy

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Authors: M. Maatar, M. Mekadem, M. Medale, B. Hadjed, B. Imine

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In this paper, numerical simulations have been carried out to study the performances of a flapping wing used as an energy collector. Metamodeling and genetic algorithms are used to detect the optimal configuration, improving power coefficient and/or efficiency. Radial basis functions and genetic algorithms have been applied to solve this problem. Three optimization factors are controlled, namely dimensionless heave amplitude h₀, pitch amplitude θ₀ and flapping frequency f. ANSYS FLUENT software has been used to solve the principal equations at a Reynolds number of 1100, while the heave and pitch motion of a NACA0015 airfoil has been realized using a developed function (UDF). The results reveal an average power coefficient and efficiency of 0.78 and 0.338 with an inexpensive low-fidelity model and a total relative error of 4.1% versus the simulation. The performances of the simulated optimum RBF-NSGA-II have been improved by 1.2% compared with the validated model.

Keywords: numerical simulation, flapping wing, energy extraction, power coefficient, efficiency, RBF, NSGA-II

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Authors: Katalin Gombos, Bence Gálik, Krisztina Ildikó Kalács, Krisztina Gödöny, Ákos Várnagy, József Bódis, Attila Gyenesei, Gábor L. Kovács

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Although non-invasive pre-implantation genetic testing for aneuploidy (NIPGT-A) is potentially appropriate to assess chromosomal ploidy of the embryo, practical application of it in a routine IVF center has not been started in the absence of a recommendation. We developed a comprehensive workflow for a clinically applicable strategy for NIPGT-A based on next-generation sequencing (NGS) technology. We performed MALBAC whole genome amplification and NGS on spent blastocyst culture media of Day 3 embryos fertilized with intra-cytoplasmic sperm injection (ICSI). Spent embryonic culture media of morphologically good quality score embryos were enrolled in further analysis with the blank culture media as background control. Chromosomal abnormalities were identified by an optimized bioinformatics pipeline applying a copy number variation (CNV) detecting algorithm. We demonstrate a comprehensive workflow covering both wet- and dry-lab procedures supporting a clinically applicable strategy for NIPGT-A. It can be carried out within 48 h which is critical for the same-cycle blastocyst transfer, but also suitable for “freeze all” and “elective frozen embryo” strategies. The described integrated approach of non-invasive evaluation of embryonic DNA content of the culture media can potentially supplement existing pre-implantation genetic screening methods.

Keywords: next generation sequencing, in vitro fertilization, embryo assessment, non-invasive pre-implantation genetic testing

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Authors: Marina Franulovic, Robert Basan, Bozidar Krizan

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Constitutive modelling of material behaviour is becoming increasingly important in prediction of possible failures in highly loaded engineering components, and consequently, optimization of their design. In order to account for large number of phenomena that occur in the material during operation, such as kinematic hardening effect in low cycle fatigue behaviour of steels, complex nonlinear material models are used ever more frequently, despite of the complexity of determination of their parameters. As a method for the determination of these parameters, genetic algorithm is good choice because of its capability to provide very good approximation of the solution in systems with large number of unknown variables. For the application of genetic algorithm to parameter identification, inverse analysis must be primarily defined. It is used as a tool to fine-tune calculated stress-strain values with experimental ones. In order to choose proper objective function for inverse analysis among already existent and newly developed functions, the research is performed to investigate its influence on material behaviour modelling.

Keywords: genetic algorithm, kinematic hardening, material model, objective function

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