Search results for: biological marker

Authors: Rami Al Jafar, Paul Elliott, Konstantinos K. Tsilidis, Abbas Dehghan

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Although Ramadan fasting is a ritual that is practiced every year by millions of Muslims, studies on Ramadan fasting are still scarce. To the best of our knowledge, none of the previous studies comprehensively explored the effect on the metabolic profile. In London Ramadan Fasting Study, blood samples were collected from 81 participants before and 10-14 days after Ramadan. Blood samples were analysed using nuclear magnetic resonance (NMR) spectroscopy which covers 249 metabolites. Mixed-effects models were used to analyse collected data and assess the effect of Ramadan fasting on the metabolic profile. Our observational study involved 85 individuals with a mean age of 45.2 years, and 53.1% of them were males. After Ramadan, forty metabolites were affected significantly by Ramadan fasting. Most of these metabolites were metabolites ratios (24), and the rest were three Glycolysis, three ketone bodies, nine Lipoprotein subclasses and one inflammation marker. This study suggests that Ramadan fasting is significantly associated with changes in the metabolic profile. However, the changes are assumed to be temporary, and the long-term effect of these changes is unknown.

Keywords: metabolic profile, Ramadan fasting, metabolites, intermittent fasting

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Authors: E. Marei, A. Hammad, S. Ismail, A. El-Gindy

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This study aims to investigate the ability of different formula of mixed bacteria as a biological treatments of wastewater after primary treatment as a bio-treatment and bio-removal and bio-adsorbent of different heavy metals in natural circumstances. The wastewater was collected from Sarpium forest site-Ismailia Governorate, Egypt. These treatments were mixture of free cells and mixture of immobilized cells of different bacteria. These different formulas of mixed bacteria were prepared under Lab. condition. The obtained data indicated that, as a result of wastewater bio-treatment, the removal rate was found to be 76.92 and 76.70% for biological oxygen demand, 79.78 and 71.07% for chemical oxygen demand, 32.45 and 36.84 % for ammonia nitrogen as well as 91.67 and 50.0% for phosphate after 24 and 28 hrs with mixed free cells and mixed immobilized cells, respectively. Moreover, the bio-removals of different heavy metals were found to reach 90.0 and 50. 0% for Cu ion, 98.0 and 98.5% for Fe ion, 97.0 and 99.3% for Mn ion, 90.0 and 90.0% Pb, 80.0% and 75.0% for Zn ion after 24 and 28 hrs with mixed free cells and mixed immobilized cells, respectively. The results indicated that 13.86 and 17.43% of removal efficiency and reduction of total dissolved solids were achieved after 24 and 28 hrs with mixed free cells and mixed immobilized cells, respectively.

Keywords: wastewater bio-treatment , bio-sorption heavy metals, biological desalination, immobilized bacteria, free cell bacteria

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Authors: Laetitia Lemiere, Marie Gosme, Gerard Subsol, Marc Jaeger

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Agroforestry is recognized as a way of developing sustainable and resilient agriculture that can fight against climate change. However, the number of species combinations, spatial configurations, and management options for trees and crops is vast. These choices must be adapted to the pedoclimatic and socio-economic contexts and to the objectives of the farmer, who therefore needs support in designing his system. Participative design workshops are a good way to integrate the knowledge of several experts in order to design such complex systems. The design of agroforestry systems should take into account both spatial aspects (e.g., spacing of trees within the lines and between lines, tree line orientation, tree-crop distance, species spatial patterns) and temporal aspects (e.g., crop rotations, tree thinning and pruning, tree planting in the case of successional agroforestry). Furthermore, the interactions between trees and crops evolve as the trees grow. However, agroforestry design workshops generally emphasize the spatial aspect only through the use of static tokens to represent the different species when designing the spatial configuration of the system. Augmented reality (AR) may overcome this limitation, allowing to visualize dynamic representations of trees and crops, and also their interactions, while at the same time retaining the possibility to physically interact with the system being designed (i.e., move trees, add or remove species, etc.). We propose an ergonomic digital solution capable of assisting a group of agroforestry experts to design an agroforestry system and to represent it. We investigated the use of web-based marker-based AR that does not require specific hardware and does not require specific installation so that all users could use their own smartphones right out of the pocket. We developed a prototype mobilizing the AR.js, ArToolKit.js, and Three.js open source libraries. In our implementation, we gradually build a virtual agroforestry system pattern scene from the users' interactions. A specific set of markers initialize the scene properties, and the various plant species are added and located during the workshop design session. The full virtual scene, including the trees positions with their neighborhood, are saved for further uses, such as virtual, augmented instantiation in the farmer fields. The number of tree species available in the application is gradually increasing; we mobilize 3D digital models for walnut, poplar, wild cherry, and other popular species used in agroforestry systems. The prototype allows shadow computations and the representation of trees at various growth stages, as well as different tree generations, and is thus able to visualize the dynamics of the system over time. Future work will focus on i) the design of complex patterns mobilizing several tree/shrub organizations, not restricted to lines; ii) the design of interfaces related to cultural practices, such as clearing or pruning; iii) the representation of tree-crop interactions. Beside tree shade (light competition), our objective is to represent also below-ground competitions (water, nitrogen) or other variables of interest for the design of agroforestry systems (e.g., predicted crop yield).

Keywords: agroforestry system design, augmented reality, marker-based AR, participative design, web-based AR

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Authors: Abdelkader Anouzla, Soukaina Bouaouda, Roukaya Bouyakhsass, Salah Souabi, Abdeslam Taleb

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During storage and under the combined action of rainwater and natural fermentation, these wastes produce over 800.000 m3 of landfill leachates. Due to population growth and changing global economic activities, the amount of waste constantly generated increases, making more significant volumes of leachate. Leachate, when leaching into the soil, can negatively impact soil, surface water, groundwater, and the overall environment and human life. The leachate must first be treated because of its high pollutant load before being released into the environment. This article reviews the different leachate treatments in September 2022 techniques. Different techniques can be used for this purpose, such as biological, physical-chemical, and membrane methods. Young leachate is biodegradable; in contrast, these biological processes lose their effectiveness with leachate aging. They are characterized by high ammonia nitrogen concentrations that inhibit their activity. Most physical-chemical treatments serve as pre-treatment or post-treatment to complement conventional treatment processes or remove specific contaminants. After the introduction, the different types of pollutants present in leachates and their impacts have been made, followed by a discussion highlighting the advantages and disadvantages of the various treatments, whether biological, physicochemical, or membrane. From this work, due to their simplicity and reasonable cost compared to other treatment procedures, biological treatments offer the most suitable alternative to limit the effects produced by the pollutants in landfill leachates.

Keywords: landfill leachate, landfill pollution, impact, wastewater

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Authors: Pardeep Singh, Kamlesh Dutta

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Many languages have fixed sentence structure and others are free word order. The accuracy of anaphora resolution of syntax based algorithm depends on structure of the sentence. So, it is important to analyze the structure of any language before implementing these algorithms. In this study, we analyzed the sentence structure exploiting the case marker in Hindi as well as some special tag for subject and object. We also investigated the word order for Hindi. Word order typology refers to the study of the order of the syntactic constituents of a language. We analyzed 165 news items of Ranchi Express from EMILEE corpus of plain text. It consisted of 1745 sentences. Eight file of dialogue based from the same corpus has been analyzed which will have 1521 sentences. The percentages of subject object verb structure (SOV) and object subject verb (OSV) are 66.90 and 33.10, respectively.

Keywords: anaphora resolution, free word order languages, SOV, OSV

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Authors: AnnWon Chew, Nik Norulaini Nik Ab Rahman, Mohd Omar Ab Kadir, C. C. Chen, Jaafar Chua

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This paper presents an innovative process to solve the ammonia, nitrite and nitrate build-up problem in recirculating system using Biological Aquaculture System (BAS). The novel aspects of the process lie in a series of bioreactors that specially arrange and design to meet the required conditions for water purification. The BAS maximizes the utilization of bio-balls as the ideal surface for beneficial microbes to flourish. It also serves as a physical barrier that traps organic particles, which in turn becomes source for the microbes to perform their work. The operation in the proposed system gives a low concentration and average range of good maintain excellent water quality, i.e., with low levels of ammonia, nitrite, nitrate, a suitable pH range for aquaculture and low turbidity. The BAS thus provides a solution for sustainable small-scale, urban aquaculture operation with a high recovery water and minimal waste disposal.

Keywords: ammonia, bioreactor, Biological Aquaculture System (BAS), bio-balls, water recirculating technology

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Authors: Li Kewen, Su Zhaoxin, Wang Xingmou, Zhu Jian Bing

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Conventional reservoir prediction methods ar not sufficient to explore the implicit relation between seismic attributes, and thus data utilization is low. In order to improve the predictive classification accuracy of reservoir lithology, this paper proposes a deep learning lithology prediction method based on ResNet (Residual Neural Network) and SENet (Squeeze-and-Excitation Neural Network). The neural network model is built and trained by using seismic attribute data and lithology data of Shengli oilfield, and the nonlinear mapping relationship between seismic attribute and lithology marker is established. The experimental results show that this method can significantly improve the classification effect of reservoir lithology, and the classification accuracy is close to 70%. This study can effectively predict the lithology of undrilled area and provide support for exploration and development.

Keywords: convolutional neural network, lithology, prediction of reservoir, seismic attributes

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Authors: Meriche Hacene

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Introduction: Celiac disease (CD) is a chronic immune-mediated enteropathy triggered by gluten found in wheat or oats or rye. Celiac disease is associated with the HLA-DQ2 and HLA-DQ8 susceptibility alleles. This association with the HLA DQ2/DQ8 molecules confirmed the responsibility of genetic factors that intervene in the triggering of the autoimmune process of this condition. Objective: To evaluate the results of HLA DQ2 and HLA DQ8 typing of 40 patients suspected of having CD by PCR-SSP (Polymerase Chain Reaction Sequence Specific Primers). Material and method : 40 patients suspected of celiac disease with IgA transglutaminase serology (-) and duodenal biopsy (+). HLADR/DQ PCR-SSP (fluogen-innotrain) typing was carried out. Results : The average age of adults was 40 years, children: 4 years, the sex ratio was 1M/3F. In our patients the HLA DQ2 allele is found with a frequency of 75%, the DQ8 with a frequency of 25%, 17.5% were HLA-DQ2 homozygous and 15% were HLADQ2/HLADQ8. In our series, HLADQ2, DQ8 are found in almost all patients with a frequency of 95%. 30% of patients in our study had associated positivity of HLA-DRB3, DRB4 or DRB5 alleles. Conclusion : A high prevalence of positivity of HLADQ2 alleles at the expense of HLA DQ8 was found, which is consistent with literature data. These molecules constitute an additional marker for screening and diagnosis of CD.

Keywords: HLA typing, coeliac disease, HLA DQ 2, HLA DQ8

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Authors: Rana Akyazi, Cal Welbourn, Oscar E. Liburd

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The family Phytoseiidae are the most common plant inhabiting group of predatory mites. They are generally considered to be important biological control agents of pest mites on many crops world-wide. Several species of these mites are commercially available in many countries. This study was carried out to determine phytoseiid mite species on nine different blackberry varieties (Arapaho, Choctaw, Kiowa, Nachez, Navaho, Osage, Ouachita, Von, Watchita). The survey was conducted from June to October 2016. Leaf samples were collected monthly from selected organic and conventional commercial blackberry (Rubus spp.) farms in Florida and Georgia, USA. Nine phytoseiid mite (Acari: Mesostigmata) species were determined during the study. The results also showed that the incidence of Phytoseiidae was greater in organic than in conventional blackberries. Future survey studies can provide detection of new species, which may hold potential for biological control of economically important pests in key fruit crops.

Keywords: biological control, mite, Phytoseiidae, predator, Rubus spp.

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Authors: Godfrey Muiya Mukala

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This research looks at an array of fields in Sub-Saharan Africa comprising agriculture, food enterprises, medicine, organisms genetically modified, microbiology, and nanotechnology that can be gained from biotechnological research and development. Findings into dangerous organisms, mainly bacterial germs, rickettsia, fungi, parasites, or organisms that are genetically engineered, have immensely posed questions attributed to the biological danger they bring forth to human beings and the environment because of their uncertainties. In addition, the recurrence of previously managed diseases or the inception of new diseases are connected to biosafety challenges, especially in rural set-ups in low and middle-income countries. Notably, biotechnology laboratories are required to adopt biosafety measures to protect their workforce, community, environment, and ecosystem from unforeseen materials and organisms. Sensitization and inclusion of educational frameworks for laboratory workers are essential to acquiring a solid knowledge of harmful biological agents. This is in addition to human pathogenicity, susceptibility, and epidemiology to the biological data used in research and development. This article reviews and analyzes research intending to identify the proper implementation of universally accepted practices in laboratory safety and biological hazards. This research identifies ideal microbiological methods, adequate containment equipment, sufficient resources, safety barriers, specific training, and education of the laboratory workforce to decrease and contain biological hazards. Subsequently, knowledge of standardized microbiological techniques and processes, in addition to the employment of containment facilities, protective barriers, and equipment, is far-reaching in preventing occupational infections. Similarly, reduction of risks and prevention may be attained by training, education, and research on biohazards, pathogenicity, and epidemiology of the relevant microorganisms. In this technique, medical professionals in rural setups may adopt the knowledge acquired from the past to project possible concerns in the future.

Keywords: sub-saharan africa, biotechnology, laboratory, infections, health

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Authors: Ouchemoukh Salim, Amessis-Ouchemoukh Nadia, Guenaoui Nawel, Moumeni Lynda, Zaidi Hicham, Otmani Amar, Sadou Dyhia

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Honey is a hive food rich in carbohydrates and water and it also has a lot of nutrients (enzymes, minerals, organic acids, phytochemicals...). It is used in different nutritional and therapeutic fields. Algerian honey was studied for its physicochemical parameters, nutritional values (moisture, brix, pH, electrical conductivity, and amounts of HMF, proteins, proline, total phenolic compounds and flavonoids) and some biological activities (antioxidant, anti-inflammatory and enzymatic anti-browning). The antioxidant activities of the samples were estimated using different methods (ABTS, DPPH free radicals scavenging, reducing power, and chelating ferrous activity). All honeys were acidic (3.45≤pH≤4.65). The color varied from mimosa yellow to dark brown. The specific rotation was levorotatory in most honey samples, and the electrical conductivity, hydroxymethylfurfural, and proline values agreed with the international honey requirements. For anti-inflammatory activity, the results showed that the inhibiting capacity of the denaturation of the BSA of the honey analyzed varied from 15 to 75 % with a maximum of activity at the concentration of 0,5 mg/ml. All honey exhibited enzymatic anti-browning on different slices of fruits. In fact, the results showed that the controls have the greatest browning unit compared to the honeys studied and PPO and POD enzymes had the lowest enzyme activity. High significant correlations were found between the color of honey, its antioxidant content and its biological activities (antioxidant, anti-inflammatory and enzymatic anti-browning). The dark color of honey is a good indicator of the best biological properties, therefore, the best nutritional and therapeutic values.

Keywords: honey, physico-chemical parameters, bioactive compounds, biological properties

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Authors: Sevil Arabaci Tamer, Gonul Gurol, Ibrahim Tekeoglu, Halil Harman, Ihsan Hakki Ciftci

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Neuroserpin (NSP) is a serine protease inhibitor and member of the serpin family. It is expressed in developing and adult nervous systems, and acts as an inhibitor of protease tissue plasminogen activator (tPA) and a regulator of neuronal growth and plasticity. Also NSP displays anti-inflammatory activity. But, its role in rheumatoid arthritis had never been studied before. So, the aim of the present study was to investigate the effect of neuroserpin in patients with RA. A total of 50 frozen (-20 ºC) serum samples 40 of them belonged to patients with RA, and 10 sample belonged to healthy subjects, were enrolled prospectively. We used DAS-28 to evaluate disease activity. The following clinical data gathered from the original patients' charts. Serum neuroserpin levels were measured by enzyme-linked immunosorbent assay. Our preliminary study results demonstrate, for the first time, that NSP levels are significantly different in RA patients relative to healthy subjects (P = 0.014). So, NSP contribute to pathological condition of RA. Thus, we believe that serum NSP levels can be as a marker in patients with RA. However other inflammatory diseases should be further investigated.

Keywords: neuroserpin, rheumatoid arthritis, tPA, tPA inhibitor

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Authors: Chandra Mukherjee

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The prevalent knowledge of the biological systems is based on the standard scientific perception of natural equilibrium, determination and predictability. Recently, a rethinking of concepts was presented and a new scientific perspective emerged that involves complexity theory with deterministic chaos theory, nonlinear dynamics and theory of fractals. The unpredictability of the chaotic processes probably would change our understanding of diseases and their management. The mathematical definition of chaos is defined by deterministic behavior with irregular patterns that obey mathematical equations which are critically dependent on initial conditions. The chaos theory is the branch of sciences with an interest in nonlinear dynamics, fractals, bifurcations, periodic oscillations and complexity. Recently, the biomedical interest for this scientific field made these mathematical concepts available to medical researchers and practitioners. Any biological network system is considered to have a nominal state, which is recognized as a homeostatic state. In reality, the different physiological systems are not under normal conditions in a stable state of homeostatic balance, but they are in a dynamically stable state with a chaotic behavior and complexity. Biological systems like heart rhythm and brain electrical activity are dynamical systems that can be classified as chaotic systems with sensitive dependence on initial conditions. In biological systems, the state of a disease is characterized by a loss of the complexity and chaotic behavior, and by the presence of pathological periodicity and regulatory behavior. The failure or the collapse of nonlinear dynamics is an indication of disease rather than a characteristic of health.

Keywords: HRV, HRVI, LF, HF, DII

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Authors: L. Kashyap, S. Jha, D. Shende, V. K. Mohan, P. Khanna, A. Aravindan, S. Kashyap, L. Singh, S. Aggarwal

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Obesity is associated with a chronic inflammatory state. During surgery, there is an interplay between anaesthetic and surgical stress vis-a-vis the already present complex immune state. Moreover, the postoperative period is dictated by inflammation, which is crucial for wound healing and regeneration. An excess of inflammatory response might hamper recovery besides increasing the risk for infection and complications. There is definite evidence of the immunosuppressive role of inhaled anaesthetic agents. This immune modulation may be brought into effect directly by influencing the innate and adaptive immunity cells. The effects of propofol on immune mechanisms in has been widely elucidated because of its popularity. It reduces superoxide generation, elastase release, and chemotaxis. However, there is no unequivocal proof of one’s superiority over the other. Hence, an anaesthetic regimen with lesser inflammatory potential and specific to the obese patient is needed. OBESITA trial protocol (2019) by Sousa and co-workers in progress aims to test the hypothesis that anaesthesia with sevoflurane results in a weaker proinflammatory response compared to propofol, as evidenced by lower IL-6 and other biomarkers and an increased macrophage differentiation into M2 phenotype in adipose tissue. IL-6 was used as the objective parameter to evaluate inflammation as it is regulated by both surgery and anesthesia. It is the most sensitive marker of the inflammatory response to tissue damage since it is released within minutes by blood leukocytes. We hypothesized that maintenance of anaesthesia with propofol would lead to less inflammation than that with desflurane. Aims: The effect of two anaesthetic techniques, total intravenous anaesthesia (TIVA) with propofol and desflurane, on surgical stress response was evaluated. The primary objective was to compare serum interleukin-6 (IL-6) levels before and after surgery. Methods: In this prospective single-blinded randomized controlled trial undertaken, 30 obese patients (BMI>30 kg/m2) undergoing laparoscopic bariatric surgery under general anaesthesia were recruited. Patients were randomized to receive desflurane or TIVA using a target-controlled infusion for maintenance of anaesthesia. As a marker of inflammation, pre-and post-surgery IL-6 levels were compared. Results: After surgery, IL-6 levels increased significantly in both groups. The rise in IL-6 was less with TIVA than with desflurane; however, it did not reach significance. IL-6 rise post-surgery correlated positively with the complexity of procedure and duration of surgery and anaesthesia, rather than anaesthetic technique. Both groups did not differ in terms of intra-operative hemodynamic and respiratory variables, time to awakening, postoperative pulmonary complications, and duration of hospital stay. The incidence of nausea was significantly higher with desflurane than with TIVA. Conclusion: Inflammatory response did not differ as a function of anaesthetic technique when propofol and desflurane were compared. Also, patient and surgical variables dictated post-operative inflammation more than the anaesthetic factors. Further, larger sample size is needed to confirm or refute these findings.

Keywords: bariatric, biomarkers, inflammation, laparoscopy

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Authors: Ryeong-Hyeon Kim, Ah-Reum Lee, Seong-Soo Roh, Gyo-Nam Kim

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Appropriate regulation of melanogenesis is important for the management of skin pigmentation-related disease. Although several beneficial effects of fisetin (3,7,3’,4’-tetrahydroxyflavone) have been reported, the precise role and molecular mechanisms of fisetin in skin health both remain unclear. Here, we induced melanogenesis of HRM2 mice (n=7/group) by UVB irradiation for 20 days. UVB-induced HRM2 mice showed that the significantly increased melanin accumulation, however, fisetin treatment (25mg and 50mg/kg of body weight) dose-dependently and significantly inhibits UVB-induced melanogenesis. In line with this, fisetin treatment effectively down-regulated m RNA and expression levels of tyrosinase, TRP2, and MITF. In addition, our inhibitor assay revealed the down-regulated melanogenic marker genes by fisetin treatment were mediated with connective tissue growth factor (CCN2)/TGF-β signaling pathway. Useful information is provided for development of functional foods using fisetin for skin health.

Keywords: connective tissue growth factor, fisetin, melanogenesis, skin, TGF-beta

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Authors: Abdulkareem M. Hamid, Yaseen Elhebshi, Adam Daïch

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Luotonins and its derivatives (Isoluotonins) are alkaloids from the aerial parts of Peganum nigellastrum Bunge that display three major skeleton types. Luotonins A, B, and E are pyrroloquinazolinoquinoline alkaloids. A few methods were known for the sysnthesis of Isoluotonin. All luotonins have shown promising cytotoxicities towards selected human cancer cell lines, especially against leukemia P-388 cells. Luotonin A is the most active one, with its activity stemming from topoisomerase I-dependent DNA-cleavage. Such intriguing biological activities and unique structures have led not only to the development of synthetic methods for the efficient synthesis of these compounds, but also to interest in structural modifications for improving the biological properties. Recent progress in the study of luotonins is covered.

Keywords: luotonin A, isoluotonin, pyrroloquiolines, alkaloids

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Authors: Roberto Rubem Silva-Brandao, Aurea Maria Zollner Ianni

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This article discusses the use and the incorporation of Pre-exposure Prophylaxis for HIV (PrEP) within a risk society context. Considering contemporary social theoreticians, we discuss implications of biotechnological uses for health enhancement. Firstly, we explore examples of biological manipulation and its consequences of use on given ecological dynamics, particularly taking into account other Sexually Transmitted Infections. In addition, we discuss how HIV resistance cases occurred with people on PrEP and its possible consequences on population-based interventions. Moreover, we present recent studies that analyze biological modifications on bodies of those who are on consistent use of PrEP, and how these body modifications are addressed on common practices of Public Health. Secondly, we present our theoretical references, which are intended to the analysis that situates our contemporary society in the reflexive stage of modernization. We discuss limits of biological use by individuals and how this can fabric feelings of freedom and autonomy within the individualization process and health. Finally, we argue that biotechnological uses on health, specifically on Public Health, tackling the risk aspects of its application, shows that another sanitary pact is needed.

Keywords: PrEP, public health, social sciences, risk society

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Authors: Murad Almadani, Khalil Abu-Hantash, Xinyu Wang, Herbert Jelinek, Kinda Khalaf

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Gait analysis is used by healthcare professionals as a tool to gain a better understanding of the movement impairment and track progress. In most circumstances, monitoring patients in their real-life environments with low-cost equipment such as cameras and wearable sensors is more important. Inertial sensors, on the other hand, cannot provide enough information on angular dynamics. This research offers a method for tracking 2D joint coordinates using cutting-edge vision algorithms and a single RGB camera. We provide an end-to-end comprehensive deep learning pipeline for marker-less gait parameter estimation, which, to our knowledge, has never been done before. To make our pipeline function in real-time for real-world applications, we leverage the AlphaPose human posture prediction model and a deep learning transformer. We tested our approach on the well-known GPJATK dataset, which produces promising results.

Keywords: gait analysis, human pose estimation, deep learning, real time gait estimation, AlphaPose, transformer

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Authors: Nam-Kuk Kim, Jin Kim, Soomin Park, Changhee Lee, Mijin Chu, Seong-Hun Lee

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In this study, we conducted whole genome re-sequencing of 10 cultivars originated from five countries including Korea, China, India, Pakistan and Ethiopia with Sesamum indicum (Zhongzho No. 13) genome as a reference. Almost 80% of the whole genome sequences of the reference genome could be covered by sequenced reads. Numerous SNP and InDel were detected by bioinformatic analysis. Among these variants, 266,051 SNPs were identified as unique to countries. Pakistan and Ethiopia had high densities of SNPs compared to other countries. Three main clusters (cluster 1: Korea, cluster 2: Pakistan and India, cluster 3: Ethiopia and China) were recovered by neighbor-joining analysis using all variants. Interestingly, some variants were detected in DGAT1 (diacylglycerol O-acyltransferase 1) and FADS (fatty acid desaturase) genes, which are known to be related with fatty acid synthesis and metabolism. These results can provide useful information to understand the regional characteristics and develop DNA markers for origin discrimination of sesame.

Keywords: Sesamum indicum, NGS, SNP, DNA marker

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Authors: Salma A. Mahmoud

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Epigenetic, or alteration in gene expression influenced by extragenetic factors, has emerged as one of the most promising areas that will address some of the gaps in our current knowledge in understanding patterns of human variation. In the last decade, the research investigating epigenetic mechanisms in many fields has flourished and witnessed significant progress. It paved the way for a new era of integrated research especially between anthropology/archeology and life sciences. Skeletal remains are considered the most significant source of information for studying human variations across history, and by utilizing these valuable remains, we can interpret the past events, cultures and populations. In addition to archeological, historical and anthropological importance, studying bones has great implications in other fields such as medicine and science. Bones also can hold within them the secrets of the future as they can act as predictive tools for health, society characteristics and dietary requirements. Bones in their basic forms are composed of cells (osteocytes) that are affected by both genetic and environmental factors, which can only explain a small part of their variability. The primary objective of this project is to examine the epigenetic landscape/signature within bones of archeological remains as a novel marker that could reveal new ways to conceptualize chronological events, gender differences, social status and ecological variations. We attempted here to address discrepancies in common variants such as methylome as well as novel epigenetic regulators such as chromatin remodelers, which to our best knowledge have not yet been investigated by anthropologists/ paleoepigenetists using plethora of techniques (biological, computational, and statistical). Moreover, extracting epigenetic information from bones will highlight the importance of osseous material as a vector to study human beings in several contexts (social, cultural and environmental), and strengthen their essential role as model systems that can be used to investigate and construct various cultural, political and economic events. We also address all steps required to plan and conduct an epigenetic analysis from bone materials (modern and ancient) as well as discussing the key challenges facing researchers aiming to investigate this field. In conclusion, this project will serve as a primer for bioarcheologists/anthropologists and human biologists interested in incorporating epigenetic data into their research programs. Understanding the roles of epigenetic mechanisms in bone structure and function will be very helpful for a better comprehension of their biology and highlighting their essentiality as interdisciplinary vectors and a key material in archeological research.

Keywords: epigenetics, archeology, bones, chromatin, methylome

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Authors: Hanan Alsaeid Alshenawy

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Background: Cervical dysplasia, which is potentially precancerous, has increased in young women. Detection of cervical is important for reducing morbidity and mortality in cervical cancer. This study analyzes the immunohistochemical expression of p16, HPV L1 capsid protein and Ki67 in cervical intraepithelial lesions and correlates them with lesion grade to develop a set of markers for diagnosis and detect the prognosis of cervical cancer precursors. Methods: 75 specimens were analyzed including 15 cases CIN 1, 28 CIN 2, 20 CIN 3, and 12 cervical squamous carcinoma, besides 10 normal cervical tissues. They were stained for p16, HPV L1 and Ki-67. Sensitivity, specificity, predictive values and accuracy were evaluated for each marker. Results: p16 expression increased during the progression from CIN 1 to carcinoma. HPV L1 positivity was detected in CIN 2 and decreased gradually as the CIN grade increased but disappear in carcinoma. Strong Ki-67 expression was observed with high grades CIN and carcinoma. p16, HPV L1 and Ki67 were sensitive but with variable specificity in detecting CIN lesions. Conclusions: p16, HPV L1 and Ki67 are useful set of markers in establishing the risk of high-grade CIN. They complete each other to reach accurate diagnosis and prognosis.

Keywords: p16, HPV L1, Ki67, CIN, cervical carcinoma

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Authors: Trenten Theis, Trevor Daubert, Kennedy Kluthe, Austin Nuxoll

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Staphylococcus aureus is a gram-positive bacterium responsible for an estimated 23,000 deaths in the United States and 25,000 deaths in the European Union annually. Recurring S. aureus bacteremia is associated with biofilm-mediated infections and can occur in 5 - 20% of cases, even with the use of antibiotics. Despite these infections being caused by drug-susceptible pathogens, they are surprisingly difficult to eradicate. One potential explanation for this is the presence of persister cells—a dormant type of cell that shows a high tolerance to antibiotic treatment. Recent studies have shown a connection between low intracellular ATP and persister cell formation. Specifically, this decrease in ATP, and therefore increase in persister cell formation, is due to an interrupted tricarboxylic acid (TCA) cycle. However, S. aureus persister cells’ role in pathogenesis remains unclear. Initial studies have shown that a fumC (TCA cycle gene) knockout survives challenge from aspects of the innate immune system better than wild-type S. aureus. Specifically, challenges from two antimicrobial peptides--LL-37 and hBD-3—show a log increase in survival of the fumC::N∑ strain compared to wild type S. aureus after 18 hours. Furthermore, preliminary studies show that the fumC knockout has a log more survival within a macrophage. These data lead us to hypothesize that the fumC knockout is better suited to other aspects of the innate immune system compared to wild-type S. aureus. To further investigate the mechanism for increased survival of fumC::N∑ within a macrophage, we tested bacterial growth in the presence of reactive oxygen species (ROS), reactive nitrogen species (RNS), and a low pH. Preliminary results suggest that the fumC knockout has increased growth compared to wild-type S. aureus in the presence of all three antimicrobial factors; however, no difference was observed in any single factor alone. To investigate survival within a host, a nine-day biofilm-associated catheter infection was performed on 6–8-week-old male and female C57Bl/6 mice. Although both sexes struggled to clear the infection, female mice were trending toward more frequently clearing the HG003 wild-type infection compared to the fumC::N∑ infection. One possible reason for the inability to reduce the bacterial burden is that biofilms are largely composed of persister cells. To test this hypothesis further, flow cytometry in conjunction with a persister cell marker was used to measure persister cells within a biofilm. Cap5A (a known persister cell marker) expression was found to be increased in a maturing biofilm, with the lowest levels of expression seen in immature biofilms and the highest expression exhibited by the 48-hour biofilm. Additionally, bacterial cells in a biofilm state closely resemble persister cells and exhibit reduced membrane potential compared to cells in planktonic culture, further suggesting biofilms are largely made up of persister cells. These data may provide an explanation as to why infections caused by antibiotic-susceptible strains remain difficult to treat.

Keywords: antibiotic tolerance, Staphylococcus aureus, host-pathogen interactions, microbial pathogenesis

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Authors: Darnetty Baharuddin Salleh

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Fusarium ear rot disease is one of the most important diseases of maize and not only causes significant losses but also produced harmful mycotoxins to animals and humans. A total of 141 strains of Fusarium species were isolated from maize plants showing typical ear rot symptoms in Indonesia, and Malaysia by using the semi-selective medium (peptone pentachloronitrobenzene agar, PPA). These strains were identified morphologically. For strains in Gibberella fujikuroi species complex (Gfsc), the identification was continued by using biological identification. Three species of Fusarium were morphologically identified as Fusarium in Gibberella species complex (105 strains, 74.5%), F. verticillioides (78 strains), F. proliferatum (24 strains) and F. subglutinans (3 strains) and five species from other section (36 strains, 25.5%), F. graminearum (14 strains), F. oxysporum (8 strains), F. solani ( 1 strain), and F. semitectum (13 strains). Out of 105 Fusarium species in Gfsc, 63 strains were identified as MAT-1, 25 strains as MAT-2 and 17 strains could not be identified and in crosses with nine standard testers, three mating populations of Fusarium were identified as MP-A, G. moniliformis (68 strains, 64.76%), MP-D, G. intermedia (21 strains, 20%) and MP-E, G. subglutinans (3 strains, 2.9%), and 13 strains (12.38%) could not be identified. All trains biologically identified as MP-A, MP-D, and MP-E, were identified morphologically as F. verticillioides, F. proliferatum, and F. subglutinans, respectively. Thus, the results of this study indicated that identification based on biological identification were consistent with those of morphological identification. This is the first report on the presence of MP-A, MP-D, and MP-E on ear rot-infected maize in Indonesia; MP-A and MP-E in Malaysia.

Keywords: Fusarium, MAT-1, MAT-2, MP-A, MP-D, MP-E

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Authors: Aleena Rena Onozuka, Patompong Satapornpong

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Introduction: In a Human Leukocyte Antigen (HLA)’s immune response, HLA alleles (HLA class I and class II) play a crucial role in fighting against pathogens. HLA-B*15:01 allele had a significant association with asymptomatic COVID-19 infection (p-value = 5.67 x 10-5 ; OR = 2.40 and 95% CI = 1.54 - 3.64). There was also a notable linkage between HLA-B*51:01 allele and critically ill patients with COVID-19 (p-value = 0.007 and OR = 3.38). This study has described the distribution of HLA marker alleles in Thais and sub-groups. Objective: We want to investigate the prevalence of HLA-B*15:01 and HLA-B*51:01 alleles in the Thai population. Materials and Methods: 200 healthy Thai population were included in this study from the College of Pharmacy, Rangsit University. HLA-B alleles were genotyped using the sequence-specific oligonucleotides process (PCR-SSOs). Results: We found out that HLA-B*46:01 (12.00%), HLA-B*15:02 (9.25%), HLA-B*40:01 (6.50%), HLA-B*13:01 (6.25%), and HLA-B* 38:02 (5.50%) alleles were more common than other alleles in Thai population. HLA-B*46:01 and HLA-B*15:02 were the most common allele found across four regions. Moreover, the frequency of HLA-B*15:01 and HLA-B*51:01 alleles were similarly distributed in Thai population (0.50, 5.25 %) and (p-value > 0.05), respectively. The frequencies of HLA-B*15:01 and HLA-B*51:01 alleles were not significantly different from other populations compared to the Thai population. Conclusions: We can screen for HLA-B*15:01 and HLA-B*51:01 alleles to determine the symptoms of COVID-19 since they are universal HLA-B markers. Importantly, the database of HLA markers indicates the association between HLA frequency and populations. However, we need further research on larger numbers of COVID-19 patients and in different populations.

Keywords: HLA-B*15:01, HLA-B*51:01, COVID-19, HLA-B alleles

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Authors: Angelica Salmeron Alcocer, Deifilia Ahuatzi Chacon, Felipe Rodriguez Casasola

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Polycyclic aromatic hydrocarbons (PAHs) are produced naturally (forest fires, volcanic eruptions) and human activity (burning fossil fuels). Concern for PAHs is due to their toxic, mutagenic and carcinogenic effects and so pose a potential risk to human health and ecology. Therefore these are considered the most toxic components of oil, they are highly hydrophobic, making them easily depositable on the floor, air and water. One method of removing PAHs of contaminated soil used surfactants such as Tween 80, which it has been reported as less toxic and also increases the solubility of the PAH compared to other surfactants, fluoranthene is a PAH with molecular formula C16H10, its name derives from the fluorescence which presents to UV light. In this paper, a study of the fluoranthene removal solubilized with Tween 80 in synthetic wastewater using a microbial community (isolated from soil of coffee plantations in the state of Veracruz, Mexico) and Fenton oxidation method was performed. The microbial community was able to use both tween 80 and fluoranthene as carbon sources for growth, when the biological treatment in batch culture was applied, 100% of fluoranthene was mineralized, this only occurred at an initial concentration of 100 ppm, but by increasing the initial concentration of fluoranthene the removal efficiencies decay and degradation time increases due to the accumulation of byproducts more toxic or less biodegradable, however when the Fenton oxidation was previously applied to the biological treatment, it was observed that removal of fluoranthene improved because it is consumed approximately 2.4 times faster.

Keywords: fluoranthene, polycyclic aromatic hydrocarbons, biological treatment, fenton oxidation

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Authors: D. O. Miranda, L. R. Azevedo, J. F. C. Cordeiro, A. H. Dos Santos, S. F. Lisboa, F. S. Guimarães, G. S. Bisson

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Background: The Colorectal cancer (CRC) is one of the most common cancers and the fourth leading cause of cancer death in the world. The prevalence of psychiatric-disorders among CRC patients, mainly depression, is high, resulting in impaired quality of life and side effects of primary treatment. High levels of proinflammatory cytokines at tumor microenvironment is a feature of CRC and the literature suggests that those mediators could contribute to the development of psychiatric disorders. Nevertheless, the ability of tumor-associated biological processes to affect the central nervous system (CNS) has only recently been explored in the context of symptoms of depression and is still not well understood. Therefore, the aim of the present study was to test the hypothesis that depressive-like behavior in an experimental model of CCR induced by N-methyl-N-nitro-N-nitrosoguanidine (MNNG) was correlated to proinflammatory profile in the periphery and in the brain. Methods: Colorectal carcinogenesis was induced in adult C57BL/6 mice (n=12) by administration of MNNG (5mg/kg, 0.1ml/intrarectal instillation) 2 times a week, for 2 week. Control group (n=12) received saline (0.1ml/intrarectal instillation). Eight weeks after beginning of MNNG administration animals were submitted to the forced swim test (FST) and the sucrose preference test for evaluation, respectively, of depressive- and anhedonia-like behaviors. After behavioral evaluation, the colon was collected and brain regions dissected (cortex-C, striatum-ST and hippocampus-HIP) for posterior evaluation of cytokine levels (IL-1β, IL-10, IL-17, and CX3CL1) by ELISA. Results: MNNG induced depressive-like behavior, represented by increased immobility time in the FST (Student t test, p < 0.05) and lower sucrose preference (Student t test, p < 0.05). Moreover, there were increased levels of IL-1β, IL-17 and CX3CL1 in the colonic tissue (Student t test, p < 0.05) and in the brain (IL-1 β in the ST and HIP, Student t test, p < 0.05; IL-17 and CX3CL1 in the C and HIP, p < 0.05). IL-10 levels, in contrast, were decreased in both the colon (p < 0.05) and the brain (C and HIP, p < 0.05). Conclusions: The results obtained in the present work support the notion that tumor growth induces neuroinflammation in stress-related brain regions and depressive-like behavior, which could be related to the high incidence of depression in colorectal carcinogenesis. This work have important clinical and research implications, taken into account that cytokine levels may be a marker promissory for the developing depression in CRC patients. New therapeutic strategies to assist in alleviating mental suffering in cancer patients might result from a better understanding of the role of cytokines in the pathophysiology of depression in these subjects.

Keywords: cytokines, brain, depression, colorectal cancer

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Authors: Habtamu Abera Goshu, Ping Yan

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Copy number variation (CNV) is a significant marker of the genetic and phenotypic diversity among individuals that accounts for complex quantitative traits of phenotype and diseases via modulating gene dosage, position effects, alteration of downstream pathways, modification of chromosome structure, and position within the nucleus and disrupting coding regions in the genome. Associating copy number variations (CNVs) with growth and gene expression are a powerful approach for identifying genomic characteristics that contribute to phenotypic and genotypic variation. A previous study using next-generation sequencing illustrated that the choline kinase beta (CHKB), Krüpple-like factor 6 (KLF6), glypican 1(GPC1), and cholinergic receptor muscarinic 3 (CHRM3) genes reside within copy number variable regions (CNVRs) of yak populations that overlap with quantitative trait loci (QTLs) of meat quality and growth. As a result, this research aimed to determine the association of CNVs of the KLF6, CHKB, GPC1, and CHRM3 genes with growth traits in the Datong yak breed. The association between the CNV types of the KLF6, CHKB, GPC1, and CHRM3 genes and the growth traits in the Datong yak breed was determined by one-way analysis of variance (ANOVA) using SPSS software. The CNV types were classified as a loss (a copy number of 0 or 1), gain (a copy number >2), and normal (a copy number of 2) relative to the reference gene, BTF3 in the 387 individuals of Datong yak. These results indicated that the normal CNV types of the CHKB and GPC1 genes were significantly (P<0.05) associated with high body length, height and weight, and chest girth in six-month-old and five-year-old Datong yaks. On the other hand, the loss CNV types of the KLF6 gene is significantly (P<0.05) associated with body weight and length and chest girth at six-month-old and five-year-old Datong yaks. In the contrary, the gain CNV type of the CHRM3 gene is highly (P<0.05) associated with body weight, length, height, and chest girth in six-month-old and five-year-old. This work provides the first observation of the biological role of CNVs of the CHKB, KLF6, GPC1, and CHRM3 genes in the Datong yak breed and might, therefore, provide a novel opportunity to utilize data on CNVs in designing molecular markers for the selection of animal breeding programs for larger populations of various yak breeds. Therefore, we hypothesized that this study provided inclusive information on the application of CNVs of the CHKB, KLF6, GPC1, and CHRM3 genes in growth traits in Datong yaks and its possible function in bovine species.

Keywords: Copy number variation, growth traits, yak, genes

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Authors: Lucia Rozumová, Ivo Šafařík, Jana Seidlerová, Pavel Kůs

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Biosorption by biological waste materials from agriculture industry could be a cost-effective technique for removing metal ions from wastewater. The performance of new biosorbent systems, consisting of the waste matrixes which were magnetically modified by iron oxide nanoparticles, for the removal of lead ions from an aqueous solution was tested. The use of low-cost and eco-friendly adsorbents has been investigated as an ideal alternative to the current expensive methods. This article deals with the removal of metal ions from aqueous solutions by modified waste products - orange peels, sawdust, peanuts husks, used tea leaves and ground coffee sediment. Magnetically modified waste materials were suspended in methanol and then was added ferrofluid (magnetic iron oxide nanoparticles). This modification process gives the predictions for the formation of the smart materials with new properties. Prepared material was characterized by using scanning electron microscopy, specific surface area and pore size analyzer. Studies were focused on the sorption and desorption properties. The changes of iron content in magnetically modified materials after treatment were observed as well. Adsorption process has been modelled by adsorption isotherms. The results show that magnetically modified materials during the dynamic sorption and desorption are stable at the high adsorbed amount of lead ions. The results of this study indicate that the biological waste materials as sorbent with new properties are highly effective for the treatment of wastewater.

Keywords: biological waste, sorption, metal ions, ferrofluid

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Authors: W. S. Lawal, T. Akande

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Abstract— Four (4) difference methods were employed to detoxify Jatropha carcas, they were physical method (it include soaking and sun drying) Chemical (the use of methylated sprit, hexane and methane). Biological (the use of Aspergillus niger and then sundry for 7days and then Bacillus lichiformis) and Combined method (the combination of chemical and biological methods). Phobol esther analysis was carried out after the detoxification methods and it was found that the combined method is better off (P<0.05). Detoxified Jatropha from each of this methods was sundry and grinded for easy inclusion into poultry feed, detoxified jatropha was included at 0%, 0.5%, 1%, 2%, 3%, 4%, and 5% but the combined method was increased up to 7% because the birds were able to tolerate it, the 0% was the control experiment. 405 day old broiler chicks was used to test the effect of detoxified Jatropha carcas on their performance, there are 5birds per treatment and there are 3 replicates, the experiment lasted for 8weeks,highest number of mortality was obtained in physical method, birds in chemical method tolerated up to 3% Jatropha carcas, biological method is better, as birds there were comfortable at 5% but the best of them is combined method the birds did very well at 7% as there were less mortality and highest weight gain was achieved here (P<0.05) and it was recommended.

Keywords: phobol esther, inclusion level, tolerance level, Jatropha carcas

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Authors: Mandeep Singh Azad.Dibyendu Chakraborty, Vikas Vohra

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Introduction: Poonch is one of the remotest districts of the Jammu and Kashmir (UT) and situated on international borders. This native poultry population in these areas is quite hardy and thrives well in adverse climatic conditions. Till date, no local breed from this area (Jammu Province) has been characterized thus present study was undertaken with the main objectives of molecular characterization of ChB6 gene in local native chicken of Poonch region located at international borders between India and Pakistan. The chicken B-cell marker (ChB6) gene has been proposed as a candidate gene in regulating B-cell development. Material and Method: RNA was isolated by Blood RNA Purification Kit (HiPura) and Trizol method from whole blood samples. Positive PCR products with size 1110 bp were selected for further purification, sequencing and analysis. The amplified PCR product was sequenced by Sangers dideoxy chain termination method. The obtained sequence of ChB6 gene of Poonchi chicken were compared by MEGAX software. BioEdit software was used to construct phylogenic tree, and Neighbor Joining method was used to infer evolutionary history. In order to compute evolutionary distance Maximum Composite Likelihood method was used. Results: The positively amplified samples of ChB6 genes were then subjected to Sanger sequencing with “Primer Walking. The sequences were then analyzed using MEGA X and BioEdit software. The sequence results were compared with other reported sequence from different breed of chicken and with other species obtained from the NCBI (National Center for Biotechnology Information). ClustalW method using MEGA X software was used for multiple sequence alignment. The sequence results of ChB6 gene of Poonchi chicken was compared with Centrocercus urophasianus, G. gallus mRNA for B6.1 protein, G. gallus mRNA for B6.2, G. gallus mRNA for B6.3, Gallus gallus B6.1, Halichoeres bivittatus, Miniopterus fuliginosus Ferringtonia patagonica, Tympanuchus phasianellus. The genetic distances were 0.2720, 0.0000, 0.0245, 0.0212, 0.0147, 1.6461, 2.2394, 2.0070 and 0.2363 for ChB6 gene of Poonchi chicken sequence with other sequences in the present study respectively. Sequencing results showed variations between different species. It was observed that AT content were higher then GC content for ChB6 gene. The lower AT content suggests less thermostable. It was observed that there was no sequence difference within the Poonchi population for ChB6 gene. The high homology within chicken population indicates the conservation of ChB6 gene. The maximum difference was observed with Miniopterus fuliginosus (Eastern bent-wing bat) followed by Ferringtonia patagonica and Halichoeres bivittatus. Conclusion: Genetic variation is the essential component for genetic improvement. The results of immune related gene Chb6 shows between population genetic variability. Therefore, further association studies of this gene with some prevalent diseases in large population would be helpful to identify disease resistant/ susceptible genotypes in the indigenous chicken population.

Keywords: ChB6, sequencing, ClustalW, genetic distance, poonchi chicken, SNP

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