Search results for: sequence

Authors: Lauren M. McKinnon, Justin B. Miller, Michael F. Whiting, John S. K. Kauwe, Perry G. Ridge

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Background: Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Methods: Ramp sequences were compared from 211 vertebrates (110 Mammalian and 101 non-mammalian). The presence and absence of ramp sequences were analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life taxonomy to determine the number of parallelisms and reversals that occurred, and these results were compared to what would be expected due to random chance. Lastly, aligned nucleotides in ramp sequences were compared to the rest of the sequence in order to examine possible differences in phylogenetic signal between these regions of the gene. Results: Parsimony and maximum likelihood analyses of the presence/absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, the retention index of ramp sequences is significantly higher than would be expected due to random chance (p-value = 0). A chi-square analysis of completely orthologous ramp sequences resulted in a p-value of approximately zero as compared to random chance. Discussion: Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches.

Keywords: codon usage bias, phylogenetics, phylogenomics, ramp sequence

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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: A. Shoiynbek, K. Kozhakhmet, P. Menezes, D. Kuanyshbay, D. Bayazitov

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Speech emotion recognition has received increasing research interest all through current years. There was used emotional speech that was collected under controlled conditions in most research work. Actors imitating and artificially producing emotions in front of a microphone noted those records. There are four issues related to that approach, namely, (1) emotions are not natural, and it means that machines are learning to recognize fake emotions. (2) Emotions are very limited by quantity and poor in their variety of speaking. (3) There is language dependency on SER. (4) Consequently, each time when researchers want to start work with SER, they need to find a good emotional database on their language. In this paper, we propose the approach to create an automatic tool for speech emotion extraction based on facial emotion recognition and describe the sequence of actions of the proposed approach. One of the first objectives of the sequence of actions is a speech detection issue. The paper gives a detailed description of the speech detection model based on a fully connected deep neural network for Kazakh and Russian languages. Despite the high results in speech detection for Kazakh and Russian, the described process is suitable for any language. To illustrate the working capacity of the developed model, we have performed an analysis of speech detection and extraction from real tasks.

Keywords: deep neural networks, speech detection, speech emotion recognition, Mel-frequency cepstrum coefficients, collecting speech emotion corpus, collecting speech emotion dataset, Kazakh speech dataset

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Authors: Hamdi Omar Omar, Hela Fakhfakh, Chokri Yaich

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This work reflects the integration of different techniques, such as field sampling and observations, magnetic susceptibility measurement, cyclostratigaraphy and sequence stratigraphy. The combination of these results allows us to reconstruct the environmental evolution of the Sidi Khalif Formation in the North-South Axis (NOSA), aged of Upper Tithonian, Berriasian and Lower Valanginian. Six sedimentary facies were identified and are primarily influenced by open marine sedimentation receiving increasing terrigenous influx. Spectral analysis, based on MS variation (for the outcropped section) and wireline logging gamma ray (GR) variation (for the sub-area section) show a pervasive dominance of 405-kyr eccentricity cycles with the expression of 100-kyr eccentricity, obliquity and precession. This study provides (for the first time) a precise duration of 2.4 myr for the outcropped Sidi Khalif Formation with a sedimentation rate of 5.4 cm/kyr and the sub-area section to 3.24 myr with a sedimentation rate of 7.64 cm/kyr. We outlined 27 5th-order depositional sequences, 8 Milankovitch depositional sequences and 2 major 3rd-order cycles for the outcropping section, controlled by the long eccentricity (405 kyr) cycles and the precession index cycles. This study has demonstrated the potential of MS and GR to be used as proxies to develop an astronomically calibrated time-scale for the Mesozoic era.

Keywords: Berriasian, magnetic susceptibility, orbital tuning, Sidi Khalif Formation

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Authors: Rezky Rifaini, Raden Bagus Fajriya Hakim

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This research was conducted at the Bolo primary health Care in Bima Regency. The purpose of the research is to find out the association pattern that is formed of medical record database from Bolo Primary health care’s patient. The data used is secondary data from medical records database PHC. Sequential pattern mining technique is the method that used to analysis. Transaction data generated from Patient_ID, Check_Date and diagnosis. Sequential Pattern Discovery Algorithms Using Equivalent Classes (SPADE) is one of the algorithm in sequential pattern mining, this algorithm find frequent sequences of data transaction, using vertical database and sequence join process. Results of the SPADE algorithm is frequent sequences that then used to form a rule. It technique is used to find the association pattern between items combination. Based on association rules sequential analysis with SPADE algorithm for minimum support 0,03 and minimum confidence 0,75 is gotten 3 association sequential pattern based on the sequence of patient_ID, check_Date and diagnosis data in the Bolo PHC.

Keywords: diagnosis, primary health care, medical record, data mining, sequential pattern mining, SPADE algorithm

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Authors: Ayoub Bouazza, Ali Faddouli, Said Amal, Rachid Benhida, Khaoula Khaless

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Brine waste generated from reverse osmosis (RO) desalination plants contains various valuable compounds, mainly salts, trace elements, and organic matter. These wastes are up to two times saltier than standard seawater. Therefore, there is a strong economic interest in recovering these salts. The current practice in desalination plants is to reject the brine back to the sea, which affects the marine ecosystem and the environment. Our study aims to bring forth a reliable management solution for the valorisation of waste brines. Natural evaporation, isothermal evaporation at 25°C and 50°C, and evaporation using continuous heating were used to crystallize valuable salts from a reverse osmosis desalination plant brine located on the Moroccan Atlantic coast. The crystallization sequence of the brine was studied in comparison with standard seawater. The X-Ray Diffraction (XRD) of the precipitated solid phases showed similar results, where halite was the main solid phase precipitated from both the brine and seawater. However, Jänecke diagram prediction, along with FREZCHEM simulations, showed that Kainite should crystallize before Epsomite and Carnallite. As the absence of kainite formation in many experiments in the literature has been related to the metastability of kainite and the critical relative humidity conditions, and the precipitation of K–Mg salts is very sensitive to climatic conditions. An evaporation process is proposed as a solution to achieve the predicted crystallization path and to affirm the recovery of Kainite.

Keywords: salts crystallization, reverse osmosis, solar evaporation, frezchem, ZLD

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Authors: B. S. Jatau, Baba Adama, S. I. Fadele

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Electrical resistivity investigation was carried out around Bomo area, Zaria, Kaduna state in order to study the subsurface geologic layer with a view of determining the depth to the bedrock and thickness of the geologic layers. Vertical Electrical Sounding (VES) using Schlumberger array was carried out at fifteen (15) VES stations. ABEM terrameter (SAS 300) was used for the data acquisition. The field data obtained have been analyzed using computer software (IPI2win) which gives an automatic interpretation of the apparent resistivity. The VES results revealed heterogeneous nature of the subsurface geological sequence. The geologic sequence beneath the study area is composed of hard pan top soil (clayey and sandy-lateritic), weathered layer, partly weathered or fractured basement and fresh basement. The resistivity value for the topsoil layer varies from 40Ωm to 450Ωm with thickness ranging from 1.25 to 7.5 m. The weathered basement has resistivity values ranging from 50Ωm to 593Ωm and thickness between 1.37 and 20.1 m. The fractured basement has resistivity values ranging from 218Ωm to 520Ωm and thickness of between 12.9 and 26.3 m. The fresh basement (bedrock) has resistivity values ranging from 1215Ωm to 2150Ωm with infinite depth. However, the depth of the earth’s surface to the bedrock surface varies between 2.63 and 34.99 m. The study further stressed the importance of the findings in civil engineering structures and groundwater prospecting.

Keywords: electrical resistivity, CERT (CT), vertical electrical sounding (VES), top soil (TP), weathered basement (WB), partly weathered basement (PWB), fresh basement (FB)

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Authors: Yash M. Gupta, Kittisak Buddhachat, Surin Peyachoknagul, Somjit Homchan

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The house cricket, Acheta domesticus is one of the commonly found species of field crickets. Although it is very commonly used as food and feed, the genomic information of house cricket is still missing for genetic investigation. DNA sequencing technology has evolved over the decades, and it has also revolutionized the molecular marker development for genetic analysis. In the present study, we have sequenced the whole genome of A. domesticus using illumina platform based HiSeq X Ten sequencing technology for searching simple sequence repeats (SSRs) in DNA to develop polymorphic microsatellite markers for population genetic analysis. A total of 112,157 SSRs with primer pairs were identified, 91 randomly selected SSRs used to check DNA amplification, of which nine primers were polymorphic. These microsatellite markers have shown cross-amplification with other three species of crickets which are Gryllus bimaculatus, Gryllus testaceus and Brachytrupes portentosus. These nine polymorphic microsatellite markers were used to check genetic variation for forty-five individuals of A. domesticus, Phitsanulok population, Thailand. For nine loci, the number of alleles was ranging from 5 to 15. The observed heterozygosity was ranged from 0.4091 to 0.7556. These microsatellite markers will facilitate population genetic analysis for future studies of A. domesticus populations. Moreover, the transferability of these SSR makers would also enable researchers to conduct genetic studies for other closely related species.

Keywords: cross-amplification, microsatellite markers, observed heterozygosity, population genetic, simple sequence repeats

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Authors: Cintia Midori Kaminishikawahara, Fernanda Jéssica Mendonça, Moisés Grespan, Elza Iouko Ida, Massami Shimokomaki, Adriana Lourenço Soares

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The quality of broiler breast meat is changing as a result of continuing emphasis on genetically bird’s selection for efficiently higher meat production. The consumer is experiencing a cooked product that is drier and less juicy when consumed. Breast meat has been classified as PSE (pale, soft, exudative), DFD (dark, firm, dry) and normal color meat. However, recently variations of this color have been observed and they are not in line with the specificity of the meat functional properties. Thus, the objective of this work was to report the finding of a new pale meat color group characterized as Pale, Firm and Non-exudative (PFN) based on its pH, color, meat functional properties and micro structural evaluation. Breast meat fillets samples (n=1045) from commercial line were classified into PSE (pH ≤5.8, L* ≥ 53.0), PFN (pH > 5.8 and L* ≥ 53.0) and Normal (pH >5.8 and L* < 53.0), based on pH and L* values. In sequence, a total of 30 samples of each group were analyzed for the water holding capacity (WHC) and shear force (SF). The incidence was 9.1% for PSE meat, 85.7% for PFN and 5.2% for Normal meat. The PSE meat presented lower values of WHC (P ≤ 0.05) followed in sequence by PFN and Normal samples and also the SF values of fresh PFN was higher than PSE meat (P ≤ 0.05) and similar to Normal samples. Under optical microscopy, the cell diameter was 10% higher for PFN in relation to PSE meat and similar to Normal meat. These preliminary results indicate an emerging group of breast meat and it should be considered that the Pale, Firm and Non-exudative should be considered as an ideal broiler breast meat quality.

Keywords: broiler PSE meat, light microscopy, texture, water holding capacity

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Authors: Ogbonnaya O. Iroanya, Samson T. Fakorede, Osamudiamen J. Edosa, Hadiat A. Azeez

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The human mitochondrial DNA (mtDNA) is about 17 kbp circular DNA fragments found within the mitochondria together with smaller fragments of 1200 bp known as the control region. Knowledge of variation within populations has been employed in forensic and molecular anthropology studies. The study was aimed at investigating the polymorphic nature of the two hypervariable segments (HVS) of the mtDNA, i.e., HVS1 and HVS2, and to determine the haplogroup distribution among individuals resident in Lagos, Southwestern Nigeria. Peripheral blood samples were obtained from sixty individuals who are not related maternally, followed by DNA extraction and amplification of the extracted DNA using primers specific for the regions under investigation. DNA amplicons were sequenced, and sequenced data were aligned and compared to the revised Cambridge Reference Sequence (rCRS) GenBank Accession number: NC_012920.1) using BioEdit software. Results obtained showed 61 and 52 polymorphic nucleotide positions for HVS1 and HVS2, respectively. While a total of three indels mutation were recorded for HVS1, there were seven for HVS2. Also, transition mutations predominate nucleotide change observed in the study. Genetic diversity (GD) values for HVS1 and HVS2 were estimated to be 84.21 and 90.4%, respectively, while random match probability was 0.17% for HVS1 and 0.89% for HVS2. The study also revealed mixed haplogroups specific to the African (L1-L3) and the Eurasians (U and H) lineages. New polymorphic sites obtained from the study are promising for human identification purposes.

Keywords: hypervariable region, indels, mitochondrial DNA, polymorphism, random match probability

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Authors: Ibrahim A. Elsayed, Mohamed H. Elalfy, Mostafa M. Abdalla

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A strain-based failure criterion for composite notched laminates is introduced where the most critical stress concentration factor for the anisotropic notched laminates could be related to the failure of the corresponding quasi-isotropic laminate and the anisotropy ratio of the laminate. The proposed criterion will simplify the design of composites to meet notched failure requirements by eliminating the need for the detailed specifications of the stacking sequence at the preliminary design stage. The designer will be able to design based on the stiffness of the laminate, then at a later stage, select an appropriate stacking sequence to meet the stiffness requirements. The failure strains for the notched laminates are computed using the material’s Omni-strain envelope. The concept of Omni-strain envelope concerns the region of average strain where the laminate is safe regardless of ply orientation. In this work, we use Hashin’s failure criteria and the strains around the hole are computed using Savin’s analytic solution. A progressive damage analysis study has been conducted where the failure loads for the notched laminates are computed using finite element analysis. The failure strains are computed and used to estimate the concentration factor. It is found that the correlation found using Savin’s analytic solution predicts the same ratio of concentration factors between anisotropic and quasi-isotropic laminates as the more expensive progressive failure analysis.

Keywords: anisotropy ratio, failure criteria, notched laminates, Omni-strain envelope, savin’s solution

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Authors: Bhaven N. Tandel, Athira Rajeev

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Sequencing batch reactor process is a suspended growth process operating under non-steady state conditions which utilizes a fill and draw reactor with complete mixing during the batch reaction step (after filling) and where the subsequent steps of aeration and clarification occur in the same tank. All sequencing batch reactor systems have five steps in common, which are carried out in sequence as follows, (1) fill (2) react (3) settle (sedimentation/clarification) (4) draw (decant) and (5) idle. The study was carried out in a sequencing batch reactor of dimensions 44cmx30cmx70cm with a working volume of 40 L. Mechanical stirrer of 100 rpm was used to provide continuous mixing in the react period and oxygen was supplied by fish tank aerators. The duration of a complete cycle of sequencing batch reactor was 8 hours. The cycle period was divided into different phases in sequence as follows-0.25 hours fill phase, 6 hours react period, 1 hour settling phase, 0.5 hours decant period and 0.25 hours idle phase. The study consisted of two runs, run 1 and run 2. Run 1 consisted of 6 hours aerobic react period and run 2 consisted of 3 hours aerobic react period followed by 3 hours anoxic react period. The influent wastewater used for the study had COD, BOD, NH3-N and TKN concentrations of 308.03±48.94 mg/L, 100.36±22.05 mg/L, 14.12±1.18 mg/L, and 24.72±2.21 mg/L respectively. Run 1 had an average COD removal efficiency of 41.28%, BOD removal efficiency of 56.25%, NH3-N removal efficiency of 86.19% and TKN removal efficiency of 54.4%. Run 2 had an average COD removal efficiency of 63.19%, BOD removal efficiency of 73.85%, NH3-N removal efficiency of 90.74% and TKN removal efficiency of 65.25%. It was observed that run 2 gave better performance than run 1 in the removal of COD, BOD and TKN.

Keywords: municipal waste water, aerobic, anoxic, sequencing batch reactor

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Authors: Minhas Alam, Muhammad Hidayat Rasool, Mohsin Khurshid, Bilal Aslam

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Acinetobacter baumannii is a notorious bacterial pathogen that is an emerging nightmare in clinical settings and is mainly involved in severe nosocomial infections. However, the data related to carbapenem-resistant A. baumannii (CRAB) from veterinary settings is limited, especially in developing countries like Pakistan. To investigate the genetic diversity and molecular basis of carbapenem resistance in Acinetobacter baumannii isolates from Cattle, a total of 1960 samples were collected from cattle from Punjab, Pakistan. The isolates were analyzed by routine microbiological procedures and confirmed by polymerase chain reaction (PCR). The isolates were further screened for antimicrobial susceptibility and the presence of multiple antimicrobial-resistant determinants by PCR. Multilocus sequence typing (MLST) was performed. The results of the current study revealed that the overall prevalence of A. baumannii in cattle was 3.28% (65/1980). Among cattle 27.7% (18/65) were found CRAB strains. The CRAB isolates harbor class D β- lactamases genes, e-g, blaOXA-23 and blaOXA-51, 94.4% (17/18). CRAB isolates carry class B β- lactamases gene blaIMP, and only one isolate carries the blaNDM-1 gene. The MLST results of CRAB isolates from cattle demonstrated 5 STs and one new ST. The commonly found sequence types in CRAB isolates were ST2 (n=10, 55.5%), followed by ST642 (n=5, 27.8%) and ST600 & ST889 (n=1, 5.55%). The presence of CRAB isolates in cattle indicates an alarming situation in Punjab, Pakistan. Immediate control measures should be taken to stop the transmission of CRAB isolates within cattle, to the environment, and to clinical settings.

Keywords: acinetobacter baumannii, carbapenemases, veterinary, drug resistance

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Authors: Kieren Luellman, Makenzi Rockwell, Eduardo Callegari, Nichole Haag, Chun Wu

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Multiple sclerosis (MS) is an autoimmune disorder that damages the myelin sheath of neurons in the central nervous system. The presence of Acinetobacter bacteria and anti-Acinetobacter antibodies in MS patients has led to the hypothesis that the bacteria may contribute to MS pathogenesis. In this study, the protein sequences of Acinetobacter baumannii were compared to five peptides from three mammalian myelin proteins, i.e., Proteolipid Protein (PLP): PLP 139-151, PLP 178-191, Myelin Basic Protein (MBP): MBP 84-104 and Myelin Oligodendrocyte Glycoprotein (MOG): MOG 35-55 and MOG 92-106 respectively, known to induce experimental autoimmune encephalomyelitis (EAE), a condition similar to MS. We found 11 hits (i.e., with five or more amino acid sequence similarity) in Acinetobacter baumannii, which are identical or similar to PLP139-151, 32 hits to PLP178-191, 35 to MBP 84-104, 41 hits to MOG 35-55 and 26 hits to MOG92-106. In addition, Western blotting was used to assess possible interaction between the bacterial proteins and human anti-MBP, anti-MOG, and anti-PLP antibodies produced in rabbits, corresponding to MBP 84-104, MOG 35-55, and PLP 139-151, respectively. We found that both human Polyclonal anti-MOG antibody and anti-PLP antibody recognized a protein or more proteins of the same molecular mass of around 25 kDa. in Acinetobacter baumannii. The results suggested that this/these protein(s) might potentially serve as antigen(s) to induce anti-MOG antibody and anti-PLP antibody production in mammalian B cells. The proteomic study identified 433 hits, among which the sequence of Acinetobacter baumannii protein 491 subunit A matches a previously published enzyme Acinetobacter 3-Oxoadipate CoA-Transferase, in which a fragment of its peptide was observed to recognize MS patient serum via ELISA method. Our findings might pave the road to understanding one of the pathogenesis mechanisms of MS.

Keywords: multiple sclerosis, pathogenesis, Acinetobacter baumannii, antibody recognition

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Authors: Khaled Mahmud Gaddah

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Cretaceous deposits in the southeast of the Sirt Basin of Libya occur in several grabens that formed during a major phase of rifting related to the opening of the Tethys. They include continental deposits of Early Cretaceous age that belong to the Nubian Formation and marginal to fully marine deposits of Late Cretaceous age that belong to the Lidam Formation and transitional beds. The sequence was extensively sampled from twenty-two boreholes and palynologically analysed. Much of the sequence is barren. However, subordinate shales in all formations yield diverse assemblages of poorly to well preserved and thermally middle to post mature palynomorphs. Most of the assemblages contain non-marine palynomorphs (spores, pollen, and freshwater algae), although some contain rare marine elements (dinoflagellate cysts and acritarchs). The palynofloras enabled the recognition of six assemblage zones of the late Barremian-Turonian age based on the dominant and base/top occurrences of stratigraphically useful palynomorphs: AI (Afropollisspp.-Aequitriraditesspinulosus) of late Barremian age; AIIa (Scenedesmusbifidus-S. sp.) of late Barremian?-early Aptian age; AIIb (Afropollisoperculatus-A. zonatus) of Aptian age; AIII (Crybelosporitespannuceus-Afropollisjardinus) of early Albian age; AIV (Subtilisphaera sp.-Lophosphaeridiumspp.) of Cenomanian-?Turonian age; AIV (Pediastrumbifidites-Leiosphaeridiaspp.) of Cenomanian?-Turonian age. These assemblages are comparable to others from Northern Gondwana (particularly from Libya and Egypt) and correspond to established Cretaceous palynofloral provinces. Palynofacies analysis is used to interpret the depositional environments, and five palynofacies types are recognised that reflect increasing marine influence up section.

Keywords: palynology, palynomorphs, palynofacies, tethys, sirt basin

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Authors: Aishwarya Talapuru, Sri Silpa Padmanabhuni, B. Jyoshna

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Cryptography helps in preventing threats to information security by providing various algorithms. This study introduces a new symmetric key encryption algorithm for information security which is linked with the "raagas" which means Indian traditional scale and pattern of music notes. This algorithm takes the plain text as input and starts its encryption process. The algorithm then randomly selects a raaga from the list of raagas that is assumed to be present with both sender and the receiver. The plain text is associated with the thus selected raaga and an intermediate cipher-text is formed as the algorithm converts the plain text characters into other characters, depending upon the rules of the algorithm. This intermediate code or cipher text is arranged in various patterns in three different rounds of encryption performed. The total number of rounds in the algorithm is equal to the multiples of 3. To be more specific, the outcome or output of the sequence of first three rounds is again passed as the input to this sequence of rounds recursively, till the total number of rounds of encryption is performed. The raaga selected by the algorithm and the number of rounds performed will be specified at an arbitrary location in the key, in addition to important information regarding the rounds of encryption, embedded in the key which is known by the sender and interpreted only by the receiver, thereby making the algorithm hack proof. The key can be constructed of any number of bits without any restriction to the size. A software application is also developed to demonstrate this process of encryption, which dynamically takes the plain text as input and readily generates the cipher text as output. Therefore, this algorithm stands as one of the strongest tools for information security.

Keywords: cipher text, cryptography, plaintext, raaga

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Authors: Qinglin Liu, Zhiyong Lin, Zongheng Wei, Jianfeng Wen, Congming Yi, Hai Liu

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The multi-channel blind rendezvous problem in distributed cognitive radio networks (DCRNs) refers to how users in the network can hop to the same channel at the same time slot without any prior knowledge (i.e., each user is unaware of other users' information). The channel hopping (CH) technique is a typical solution to this blind rendezvous problem. In this paper, we propose a quinary coding and matrix structure-based CH algorithm called QCMS-CH. The QCMS-CH algorithm can guarantee the rendezvous of users using only one cognitive radio in the scenario of the asynchronous clock (i.e., arbitrary time drift between the users), heterogeneous channels (i.e., the available channel sets of users are distinct), and symmetric role (i.e., all users play a same role). The QCMS-CH algorithm first represents a randomly selected channel (denoted by R) as a fixed-length quaternary number. Then it encodes the quaternary number into a quinary bootstrapping sequence according to a carefully designed quaternary-quinary coding table with the prefix "R00". Finally, it builds a CH matrix column by column according to the bootstrapping sequence and six different types of elaborately generated subsequences. The user can access the CH matrix row by row and accordingly perform its channel, hoping to attempt rendezvous with other users. We prove the correctness of QCMS-CH and derive an upper bound on its Maximum Time-to-Rendezvous (MTTR). Simulation results show that the QCMS-CH algorithm outperforms the state-of-the-art in terms of the MTTR and the Expected Time-to-Rendezvous (ETTR).

Keywords: channel hopping, blind rendezvous, cognitive radio networks, quaternary-quinary coding

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Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

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Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

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Authors: Vivek Vaishnav, Shamim Akhtar Ansari

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Teak (Tectona grandis L.f.) belonging to plant family Lamiaceae and the most commercialized timber species is endemic to South-Asia. The adaptive fitness of the species metapopulation was evaluated through its genetic differentiation and assessing the influence of geo-climatic conditions. 290 genotypes were sampled from 29 locations of its natural distribution and the genetic data was incorporated with geo-climatic parameters. Through Bayesian approach based analysis of 43 highly polymorphic ISSR markers, six homogeneous clusters (0.8% genetic variability) were identified. The six clusters were found with the various regimes of the temperature range, i.e., I - 9.10±1.35⁰C, II -6.35±0.21⁰C, III -12.21±0.43⁰C, IV - 10.8±1.06⁰C, V - 11.67±3.04⁰C, and VI - 12.35±0.21⁰C. The population had a very high percentage of LD (21.48%) among the amplified loci possibly due to experiencing restricted gene flow as well as co-adaptation and association of distant/diverse loci/alleles as a result of the stabilized climatic conditions and countless cycles of historical recombination events on a large geological timescale. The same possibly accounts for the narrow distribution of teak as a climax species in the tropical deciduous forests of the country. The regions of strong LD in teak genome significantly associated with climatic parameters also reflect that the species is tolerant to the wide regimes of the temperature range and may possibly withstand global warming and climate change in the coming millennium.

Keywords: Bayesian analysis, inter simple sequence repeat, linkage disequilibrium, marker-geoclimatic association

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Authors: Ke Zhang, Yongli Zhu

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Due to rapid load growths in today’s highly electrified societies and the requirement for green energy sources, large-scale wind farm power transmission system is constantly developing. This system is a typical multi-terminal power supply system, whose structure of the network topology of transmission lines is complex. What’s more, it locates in the complex terrain of mountains and grasslands, thus increasing the possibility of transmission line faults and finding the fault location with difficulty after the faults and resulting in an extremely serious phenomenon of abandoning the wind. In order to solve these problems, a fault location method for multi-terminal transmission line based on wind farm characteristics and improved single-ended traveling wave positioning method is proposed. Through studying the zero sequence current characteristics by using the characteristics of the grounding transformer(GT) in the existing large-scale wind farms, it is obtained that the criterion for judging the fault interval of the multi-terminal transmission line. When a ground short-circuit fault occurs, there is only zero sequence current on the path between GT and the fault point. Therefore, the interval where the fault point exists is obtained by determining the path of the zero sequence current. After determining the fault interval, The location of the short-circuit fault point is calculated by the traveling wave method. However, this article uses an improved traveling wave method. It makes the positioning accuracy more accurate by combining the single-ended traveling wave method with double-ended electrical data. What’s more, a method of calculating the traveling wave velocity is deduced according to the above improvements (it is the actual wave velocity in theory). The improvement of the traveling wave velocity calculation method further improves the positioning accuracy. Compared with the traditional positioning method, the average positioning error of this method is reduced by 30%.This method overcomes the shortcomings of the traditional method in poor fault location of wind farm transmission lines. In addition, it is more accurate than the traditional fixed wave velocity method in the calculation of the traveling wave velocity. It can calculate the wave velocity in real time according to the scene and solve the traveling wave velocity can’t be updated with the environment and real-time update. The method is verified in PSCAD/EMTDC.

Keywords: grounding transformer, multi-terminal transmission line, short circuit fault location, traveling wave velocity, wind farm

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Authors: Iftikhar A. Tayubi, Tabrej Khan, Mansoor M. Alsubei, Fahad A. Alsaferi

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LIZTOXD provides a single source of high-quality information about proteinaceous lizard toxins that will be an invaluable resource for pharmacologists, neuroscientists, toxicologists, medicinal chemists, ion channel scientists, clinicians, and structural biologists. We will provide an intuitive, well-organized and user-friendly web interface that allows users to explore the detail information of Lizard and toxin proteins. It includes common name, scientific name, entry id, entry name, protein name and length of the protein sequence. The utility of this database is that it can provide a user-friendly interface for users to retrieve the information about Lizard, toxin and toxin protein of different Lizard species. These interfaces created in this database will satisfy the demands of the scientific community by providing in-depth knowledge about Lizard and its toxin. In the next phase of our project we will adopt methodology and by using A MySQL and Hypertext Preprocessor (PHP) which and for designing Smart Draw. A database is a wonderful piece of equipment for storing large quantities of data efficiently. The users can thus navigate from one section to another, depending on the field of interest of the user. This database contains a wealth of information on species, toxins, toxins, clinical data etc. LIZTOXD resource that provides comprehensive information about protein toxins from lizard toxins. The combination of specific classification schemes and a rich user interface allows researchers to easily locate and view information on the sequence, structure, and biological activity of these toxins. This manually curated database will be a valuable resource for both basic researchers as well as those interested in potential pharmaceutical and agricultural applications of lizard toxins.

Keywords: LIZTOXD, MySQL, PHP, smart draw

Procedia PDF Downloads 133

Authors: Khaled Igbaria

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Laila Al-Othman is a well-known feminist writer in Kuwait and the entire Arab world. She was born in 1943 in Kuwait to a large and wealthy family. The author has written several short stories, as well as novels, such as The Woman and the Cat (1985) and Wasumayya Comes out of the Sea (1986), which was chosen as one of the best 100 Arab novels of the 21st century. Another prominent novel of hers is Ṣamt al-Farāshāt [Silence of the Butterflies] (2007), which was highly controversial in her native Kuwait upon publication. For this study, her engagement in feminism was achieved by exploring the different ways in which her novel, Ṣamt al-Farāshāt [Silence of the Butterflies], addresses several feminist issues, mainly forced marriage, rape and sexual abuse, gender-based physical, sexual violence, and enforced silence. This paper focuses on demonstrating social obstacles and continuous trauma caused by a sequence of pain experienced by Arab females in their patriarchal society. This study argues that the novel reveals a sustained effort to raise the banner of feminism and a strong desire to liberate Arab women from patriarchal domination. Al-Othman successfully and uniquely represents women as gender-based traumatic victims of sexual and physical violence, forced silence, and general oppression in the patriarchal Arab society, as those needing help, support, protection, and liberation. They are not represented as independent or free. Methodologically, the study employs a qualitative literary analysis method in addition to trauma theory psychoanalysis, concentrating on feminist issues highlighted in the novel.

Keywords: Al-Othman, Arab women pain, trauma within narration., Silence of the Butterflies

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Authors: Masoud Sheidai, Fahimeh Koohdar, Hashem Sharifi

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Juglans regia (L.) commonly known as Persian walnut of the genus Juglans L. (Juglandaceae) is one of the most important cultivated plant species due to its high-quality wood and edible nuts. The genetic diversity analysis is essential for conservation and management of tree species. Persian walnut is native from South-Eastern Europe to North-Western China through Tibet, Nepal, Northern India, Pakistan, and Iran. The species like Persian walnut, which has a wide range of geographical distribution, should harbor extensive genetic variability to adapt to environmental fluctuations they face. We aimed to study the population genetic structure of seven Persian walnut populations including three wild and four cultivated populations by using ISSR (Inter simple sequence repeats) and SRAP (Sequence related amplified polymorphism) molecular markers. We also aimed to compare the genetic variability revealed by ISSR neutral multilocus marker and rDNA ITS sequences. The studied populations differed in morphological features as the samples in each population were clustered together and were separate from the other populations. Three wild populations studied were placed close to each other. The mantel test after 5000 times permutation performed between geographical distance and morphological distance in Persian walnut populations produced significant correlation (r = 0.48, P = 0.002). Therefore, as the populations become farther apart, they become more divergent in morphological features. ISSR analysis produced 47 bands/ loci, while we obtained 15 SRAP bands. Gst and other differentiation statistics determined for these loci revealed that most of the ISSR and SRAP loci have very good discrimination power and can differentiate the studied populations. AMOVA performed for these loci produced a significant difference (< 0.05) supporting the above-said result. AMOVA produced significant genetic difference based on ISSR data among the studied populations (PhiPT = 0.52, P = 0.001). AMOVA revealed that 53% of the total variability is due to among population genetic difference, while 47% is due to within population genetic variability. The results showed that both multilocus molecular markers and ITS sequences can differentiate Persian walnut populations. The studied populations differed genetically and showed isolation by distance (IBD). ITS sequence based MP and Bayesian phylogenetic trees revealed that Iranian walnut cultivars form a distinct clade separated from the cultivars studied from elsewhere. Almost all clades obtained have high bootstrap value. The results indicated that a combination of multilpcus and sequencing molecular markers can be used in genetic differentiation of Persian walnut.

Keywords: genetic diversity, population, molecular markers, genetic difference

Procedia PDF Downloads 132

Authors: Anyaphat Srithanasuwan, Noppason Pangprasit, Montira Intanon, Phongsakorn Chuammitri, Witaya Suriyasathaporn, Ynte H. Schukken

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Streptococcus uberis is one of the most common mastitis-causing pathogens, with a wide range of intramammary infection (IMI) durations and pathogenicity. This study aimed to compare shared or unique virulence factor gene clusters distinguishing persistent and transient strains of S. uberis. A total of 139 S. uberis strains were isolated from three small-holder dairy herds with a high prevalence of S. uberis mastitis. The duration of IMI was used to categorize bacteria into two groups: transient and persistent strains with an IMI duration of less than 1 month and longer than 2 months, respectively. Six representative S. uberis strains, three from each group (transience and persistence) were selected for analysis. All transient strains exhibited multi-locus sequence types (MLST), indicating a highly diverse population of transient S. uberis. In contrast, MLST of persistent strains was available in an online database (pubMLST). Identification of virulence genes was performed using whole-genome sequencing (WGS) data. Differences in genomic size and number of virulent genes were found. For example, the BCA gene or alpha-c protein and the gene associated with capsule formation (hasAB), found in persistent strains, are important for attachment and invasion, as well as the evasion of the antimicrobial mechanisms and survival persistence, respectively. These findings suggest a genetic-level difference between the two strain types. Consequently, a comprehensive study of 139 S. uberis isolates will be conducted to perform an in-depth genetic assessment through WGS analysis on an Illumina platform.

Keywords: Streptococcus Uberis, mastitis, whole genome sequence, intramammary infection, persistent S. Uberis, transient s. Uberis

Procedia PDF Downloads 20

Authors: Khin Thanda Win, Chunying Zhang, Sanghyeob Lee

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Mildew resistance locus o (Mlo), a plant-specific gene family with seven-transmembrane (TM), plays an important role in plant resistance to powdery mildew (PM). PM caused by Podosphaera xanthii is a widespread plant disease and probably represents the major fungal threat for many Cucurbits. The recent Cucurbita maxima genome sequence data provides an opportunity to identify and characterize the MLO gene family in this species. Total twenty genes (designated CmaMLO1 through CmaMLO20) have been identified by using an in silico cloning method with the MLO gene sequences of Cucumis sativus, Cucumis melo, Citrullus lanatus and Cucurbita pepo as probes. These CmaMLOs were evenly distributed on 15 chromosomes of 20 C. maxima chromosomes without any obvious clustering. Multiple sequence alignment showed that the common structural features of MLO gene family, such as TM domains, a calmodulin-binding domain and 30 important amino acid residues for MLO function, were well conserved. Phylogenetic analysis of the CmaMLO genes and other plant species reveals seven different clades (I through VII) and only clade IV is specific to monocots (rice, barley, and wheat). Phylogenetic and structural analyses provided preliminary evidence that five genes belonged to clade V could be the susceptibility genes which may play the importance role in PM resistance. This study is the first comprehensive report on MLO genes in C. maxima to our knowledge. These findings will facilitate the functional analysis of the MLOs related to PM susceptibility and are valuable resources for the development of disease resistance in pumpkin.

Keywords: Mildew resistance locus o (Mlo), powdery mildew, phylogenetic relationship, susceptibility genes

Procedia PDF Downloads 157

Authors: Igor Jerkovic

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Biodiversity of flora provides many different nectar sources for the bees. Unifloral honeys possess distinctive flavours, mainly derived from their nectar sources (characteristic volatile organic components (VOCs)). Specific or nonspecific VOCs (chemical markers) could be used for unifloral honey characterisation as addition to the melissopalynologycal analysis. The main honey volatiles belong, in general, to three principal categories: terpenes, norisoprenoids, and benzene derivatives. Some of these substances have been described as characteristics of the floral source, and other compounds, like several alcohols, branched aldehydes, and furan derivatives, may be related to the microbial purity of honey processing and storage conditions. Selection of the extraction method for the honey volatiles profiling should consider that heating of the honey produce different artefacts and therefore conventional methods of VOCs isolation (such as hydrodistillation) cannot be applied for the honey. Two-way approach for the isolation of the honey VOCs was applied using headspace solid-phase microextraction (HS-SPME) and ultrasonic solvent extraction (USE). The extracts were analysed by gas chromatography and mass spectrometry (GC-MS). HS-SPME (with the fibers of different polarity such as polydimethylsiloxane/ divinylbenzene (PDMS/DVB) or divinylbenzene/carboxene/ polydimethylsiloxane (DVB/CAR/PDMS)) enabled isolation of high volatile headspace VOCs of the honey samples. Among them, some characteristic or specific compounds can be found such as 3,4-dihydro-3-oxoedulan (in Centaurea cyanus L. honey) or 1H-indole, methyl anthranilate, and cis-jasmone (in Citrus unshiu Marc. honey). USE with different solvents (mainly dichloromethane or the mixture pentane : diethyl ether 1 : 2 v/v) enabled isolation of less volatile and semi-volatile VOCs of the honey samples. Characteristic compounds from C. unshiu honey extracts were caffeine, 1H-indole, 1,3-dihydro-2H-indol-2-one, methyl anthranilate, and phenylacetonitrile. Sometimes, the selection of solvent sequence was useful for more complete profiling such as sequence I: pentane → diethyl ether or sequence II: pentane → pentane/diethyl ether (1:2, v/v) → dichloromethane). The extracts with diethyl ether contained hydroquinone and 4-hydroxybenzoic acid as the major compounds, while (E)-4-(r-1’,t-2’,c-4’-trihydroxy-2’,6’,6’-trimethylcyclo-hexyl)but-3-en-2-one predominated in dichloromethane extracts of Allium ursinum L. honey. With this two-way approach, it was possible to obtain a more detailed insight into the honey volatile and semi-volatile compounds and to minimize the risks of compound discrimination due to their partial extraction that is of significant importance for the complete honey profiling and identification of the chemical biomarkers that can complement the pollen analysis.

Keywords: honey chemical biomarkers, honey volatile compounds profiling, headspace solid-phase microextraction (HS-SPME), ultrasonic solvent extraction (USE)

Procedia PDF Downloads 169

Authors: Daniel Zarzo Montes, Manuel Zarzo Castelló

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Proteins play a fundamental role in biology, but their structure is complex, and it is a challenge for teachers to conceptually explain the differences between their primary, secondary, tertiary, and quaternary structures. On the other hand, there are currently many computer programs to visualize the 3D structure of proteins, but they require advanced training and knowledge. Moreover, it becomes difficult to visualize the sequence of amino acids in these models, and how the protein conformation is reached. Given this drawback, a simple and instructive procedure is proposed in order to teach the protein structure to undergraduate and graduate students. For this purpose, insulin has been chosen because it is a protein that consists of 51 amino acids, a relatively small number. The methodology has consisted of the use of plastic atom models, which are frequently used in organic chemistry and biochemistry to explain the chirality of biomolecules. For didactic purposes, when the aim is to teach the biochemical foundations of proteins, a manipulative system seems convenient, starting from the chemical structure of amino acids. It has the advantage that the bonds between amino acids can be conveniently rotated, following the pattern marked by the 3D models. First, the 51 amino acids were modeled, and then they were linked according to the sequence of this protein. Next, the three disulfide bonds that characterize the stability of insulin have been established, and then the alpha-helix structure has been formed. In order to reach the tertiary 3D conformation of this protein, different interactive models available on the Internet have been visualized. In conclusion, the proposed methodology seems very suitable for biology and biochemistry students because they can learn the fundamentals of protein modeling by means of a manipulative procedure as a basis for understanding the functionality of proteins. This methodology would be conveniently useful for a biology or biochemistry laboratory practice, either at the pre-graduate or university level.

Keywords: protein structure, 3D model, insulin, biomolecule

Procedia PDF Downloads 20

Authors: Tanveer Hussain, Misbah Hussain, Masroor Ellahi Babar, Muhammad Traiq Pervez, Fiaz Hussain, Sana Zahoor, Rashid Saif

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Interleukin 2 (IL-2) is a cytokine which is produced by activated T cells, play important role in immune response against antigen. It act in both autocrine and paracrine manner. It can stimulate B cells and various other phagocytic cells like monocytes, lymphokine-activated killer cells and natural killer cells. Acting in autocrine fashion, IL-2 protein plays a crucial role in proliferation of T cells. IL-2 triggers the release of pro and anti- inflammatory cytokines by activating several pathways. In present study, exon 1 of IL-2 gene of four local Pakistani breeds (Dera Din Panah, Beetal, Nachi and Kamori) from two provinces was amplified by using reported Ovine IL-2 primers, yielding PCR product of 501 bp. The sequencing of all samples was done to identify the polymorphisms in amplified region of IL-2 gene. Analysis of sequencing data resulted in identification of one novel nucleotide substitution (T→A) in amplified non-coding region of IL-2 gene. Comparison of IL-2 gene sequence of all four breeds with other goat breeds showed high similarity in sequence. While phylogenetic analysis of our local breeds with other mammals showed that IL-2 is a variable gene which has undergone many substitutions. This high substitution rate can be due to the decreased or increased changed selective pressure. These rapid changes can also lead to the change in function of immune system. This pioneering study of Pakistani goat breeds urge for further studies on immune system of each targeted breed for fully understanding the functional role of IL-2 in goat immunity.

Keywords: interleukin 2, mutational analysis, phylogeny, goat breeds, Pakistan

Procedia PDF Downloads 578

Authors: Guillaume Bélanger, Jean-Philippe Fontaine, Clémence Hauduc

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There is an undeniable thirst from organic chemists and from the pharmaceutical industry to access complex alkaloids with short syntheses. While medicinal chemists are interested in the fascinating wide range of biological properties of alkaloids, synthetic chemists are rather interested in finding new routes to access these challenging natural products of often low availability from nature. To synthesize complex polycyclic cores of natural products, reaction cascades or sequences performed one-pot offer a neat advantage over classical methods for their rapid increase in molecular complexity in a single operation. In counterpart, reaction cascades need to be run on substrates bearing all the required functional groups necessary for the key cyclizations. Chemoselectivity is thus a major issue associated with such a strategy, in addition to diastereocontrol and regiocontrol for the overall transformation. In the pursuit of synthetic efficiency, our research group developed an innovative one-pot transformation of linear substrates into bi- and tricyclic adducts applied to the construction of Aspidospermatan-type alkaloids. The latter is a rich class of indole alkaloids bearing a unique bridged azatricyclic core. Despite many efforts toward the synthesis of members of this family, efficient and versatile synthetic routes are still coveted. Indeed, very short, non-racemic approaches are rather scarce: for example, in the cases of aspidospermidine and aspidospermine, syntheses are all fifteen steps and over. We envisaged a unified approach to access several members of the Aspidospermatan alkaloids family. The key sequence features a highly chemoselective formamide activation that triggers a Vilsmeier-Haack cyclization, followed by an azomethine ylide generation and intramolecular cycloaddition. Despite the high density and variety of functional groups on the substrates (electron-rich and electron-poor alkenes, nitrile, amide, ester, enol ether), the sequence generated three new carbon-carbon bonds and three rings in a single operation with good yield and high chemoselectivity. A detailed study of amide, nucleophile, and dipolarophile variations to finally get to the successful combination required for the key transformation will be presented. To complete the indoline fragment of the natural products, we developed an original approach. Indeed, all reported routes to Aspidospermatan alkaloids introduce the indoline or indole early in the synthesis. In our work, the indoline needs to be installed on the azatricyclic core after the key cyclization sequence. As a result, typical Fischer indolization is not suited since this reaction is known to fail on such substrates. We thus envisaged a unique photocatalyzed decarboxylative radical cyclization. The development of this reaction as well as the scope and limitations of the methodology, will also be presented. The original Vilsmeier-Haack and azomethine ylide cyclization sequence as well as the new photocatalyzed decarboxylative radical cyclization will undoubtedly open access to new routes toward polycyclic indole alkaloids and derivatives of pharmaceutical interest in general.

Keywords: Aspidospermatan alkaloids, azomethine ylide cycloaddition, decarboxylative radical cyclization, indole and indoline synthesis, one-pot sequential cyclizations, photocatalysis, Vilsmeier-Haack Cyclization

Procedia PDF Downloads 54

Authors: Ahmed F. Azmy, Amal E. Saafan, Tamer M. Essam, Magdy A. Amin, Shaban H. Ahmed

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Bacterial strains capable of degradation of malathion from the domestic sewage were isolated by an enrichment culture technique. Three bacterial strains were screened and identified as Acinetobacter baumannii (AFA), Pseudomonas aeruginosae (PS1),andPseudomonas mendocina (PS2) based on morphological, biochemical identification and 16S rRNA sequence analysis. Acinetobacter baumannii AFA was the most efficient malathion degrading bacterium, so used for further biodegradation study. AFA was able to grow in mineral salt medium (MSM) supplemented with malathion (100 mg/l) as a sole carbon source, and within 14 days, 84% of the initial dose was degraded by the isolate measured by high performance liquid chromatography. Strain AFA could also degrade other organophosphorus compounds including diazenon, chlorpyrifos and fenitrothion. The effect of different culture conditions on the degradation of malathion like inoculum density, other carbon or nitrogen sources, temperature and shaking were examined. Degradation of malathion and bacterial cell growth were accelerated when culture media were supplemented with yeast extract, glucose and citrate. The optimum conditions for malathion degradation by strain AFA were; an inoculum density of 1.5x 1012CFU/ml at 30°C with shaking. A specific polymerase chain reaction primers were designed manually using multiple sequence alignment of the corresponding carboxylesterase enzymes of Acinetobacter species. Sequencing result of amplified PCR product and phylogenetic analysis showed low degree of homology with the other carboxylesterase enzymes of Acinetobacter strains, so we suggested that this enzyme is a novel esterase enzyme. Isolated bacterial strains may have potential role for use in bioremediation of malathion contaminated.

Keywords: Acinetobacter baumannii, biodegradation, malathion, organophosphate pesticides

Procedia PDF Downloads 459