Search results for: chromosomes encoding

Authors: Sanam Preet Singh

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Music in comparison to any other art form is more reactive and alive. It has the capacity to directly interact with the listener's mind and generate an emotional response. All the major research conducted in the area majorly relied on the listener’s perspective to draw an understanding of music and its effects. There is a very small number of studies which focused on the source from which music originates, the music composers. This study aims to understand the process of how music composers understand and perceive emotions and how they translate them into music, in simpler terms how music composers encode their compositions to express determining emotions. One-to-one in-depth semi structured interviews were conducted, with 8 individuals both male and female, who were professional to intermediate-level music composers and Thematic analysis was conducted to derive the themes. The analysis showed that there is no single process on which music composers rely, rather there are combinations of multiple micro processes, which constitute the understanding and translation of emotions into music. In terms of perception of emotions, the role of processes such as Rumination, mood influence and escapism was discovered in the analysis. Unique themes about the understanding of their top down and bottom up perceptions were also discovered. Further analysis also revealed the role of imagination and emotional trigger explaining how music composers make sense of emotions. The translation process of emotions revealed the role of articulation and instrumentalization, in encoding or translating emotions to a composition. Further, applications of the trial and error method, nature influences and flow in the translation process are also discussed. In the end themes such as parallels between musical patterns and emotions, comfort zones and relatability also emerged during the analysis.

Keywords: comfort zones, escapism, flow, rumination

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Authors: Parthiban Srinivasan

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With recent advances in computational power and access to enough data in biosciences, artificial intelligence methods are increasingly being used in drug discovery research. These methods are essentially a series of advanced statistics based exercises that review the past to indicate the likely future. Our goal is to develop a model that accurately predicts biological activity and toxicity parameters for novel compounds. We have compiled a robust library of over 150,000 chemical compounds with different pharmacological properties from literature and public domain databases. The compounds are stored in simplified molecular-input line-entry system (SMILES), a commonly used text encoding for organic molecules. We utilize an automated process to generate an array of numerical descriptors (features) for each molecule. Redundant and irrelevant descriptors are eliminated iteratively. Our prediction engine is based on a portfolio of machine learning algorithms. We found Random Forest algorithm to be a better choice for this analysis. We captured non-linear relationship in the data and formed a prediction model with reasonable accuracy by averaging across a large number of randomized decision trees. Our next step is to apply deep neural network (DNN) algorithm to predict the biological activity and toxicity properties. We expect the DNN algorithm to give better results and improve the accuracy of the prediction. This presentation will review all these prominent machine learning and deep learning methods, our implementation protocols and discuss these techniques for their usefulness in biomedical and health informatics.

Keywords: deep learning, drug discovery, health informatics, machine learning, toxicity prediction

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Authors: Beata Zima, Octavio A. Márquez Reyes, Masoud Mohammadgholiha, Jochen Moll, Luca de Marchi

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This document presents the approach of using compressed sensing in signal encoding and information transferring within a guided wave sensor network, comprised of specially designed frequency steerable acoustic transducers (FSATs). Wave propagation in a damaged plate was simulated using commercial FEM-based software COMSOL. Guided waves were excited by means of FSATs, characterized by the special shape of its electrodes, and modeled using PIC255 piezoelectric material. The special shape of the FSAT, allows for focusing wave energy in a certain direction, accordingly to the frequency components of its actuation signal, which makes available a larger monitored area. The process begins when a FSAT detects and records reflection from damage in the structure, this signal is then encoded and prepared for transmission, using a combined approach, based on Compressed Sensing Matching Pursuit and Quadrature Amplitude Modulation (QAM). After codification of the signal is in binary chars the information is transmitted between the nodes in the network. The message reaches the last node, where it is finally decoded and processed, to be used for damage detection and localization purposes. The main aim of the investigation is to determine the location of detected damage using reconstructed signals. The study demonstrates that the special steerable capabilities of FSATs, not only facilitate the detection of damage but also permit transmitting the damage information to a chosen area in a specific direction of the investigated structure.

Keywords: data compression, ultrasonic communication, guided waves, FEM analysis

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Authors: Kyung-Tae Lee, Li Li Wang, Kwang-Woo Jung, Yong-Sun Bahn

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Microtubules are involved in mechanical support, cytoplasmic organization as well as in a number of cellular processes by interacting with diverse microtubule-associated proteins (MAPs), such as plus-end tracking proteins, motor proteins, and tubulin-folding cofactors. A common feature of these proteins is the presence of a cytoskeleton-associated protein-glycine-rich (CAP-Gly) domain, which is evolutionarily conserved and generally considered to bind to α-tubulin to regulate functions of microtubules. However, there has been a dearth of research on CAP-Gly proteins in fungal pathogens, including Cryptococcus neoformans, which causes fatal meningoencephalitis globally. In this study, we identified five CAP-Gly proteins encoding genes in C. neoformans. Among these, Cgp1, encoded by CNAG_06352, has a unique domain structure that has not been reported before in other eukaryotes. Supporting the role of Cpg1 in microtubule-related functions, we demonstrate that deletion or overexpression of CGP1 alters cellular susceptibility to thiabendazole, a microtubule destabilizer, and Cgp1 is co-localized with cytoplasmic microtubules. Related to the cellular functions of microtubules, Cgp1 also governs maintenance of membrane stability and genotoxic stress responses. Furthermore, we demonstrate that Cgp1 uniquely regulates sexual differentiation of C. neoformans with distinct roles in the early and late stage of mating. Our domain analysis reveals that the CAP-Gly domain plays major roles in all the functions of Cgp1. Finally, the cgp1Δ mutant is attenuated in virulence. In conclusion, this novel CAP-Gly protein, Cgp1, has pleotropic roles in regulating growth, stress responses, differentiation and pathogenicity of C. neoformans.

Keywords: human fungal pathogen, CAP-Glycine protein, microtubule, meningoencephalitis

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Authors: Fahad Almehmadi, Abdullah Alrajhi, Bader K. Alaslab, Abdullah A. Al Qurashi, Hattan A. Hassani

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Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy (ARVD/C) is an uncommon, inheritable cardiac disorder characterized by the progressive substitution of cardiac myocytes by fibro-fatty tissues. This pathologic substitution predisposes patients to ventricular arrhythmias and right ventricular failure. The underlying genetic defect predominantly involves genes encoding for desmosome proteins, particularly plakophilin-2 (PKP2). These aberrations lead to impaired cell adhesion, heightening the susceptibility to fibrofatty scarring under conditions of mechanical stress. Primarily, ARVD/C affects the right ventricle, but it can also compromise the left ventricle, potentially leading to biventricular heart failure. Clinical presentations can vary, spanning from asymptomatic individuals to those experiencing palpitations, syncopal episodes, and, in severe instances, sudden cardiac death. The establishment of a diagnostic criterion specifically tailored for ARVD/C significantly aids in its accurate diagnosis. Nevertheless, the task of early diagnosis is complicated by the disease's frequently asymptomatic initial stages, and the overall rarity of ARVD/C cases reported globally. In some cases, as exemplified by the adult female patient in this report, the disease may advance to terminal stages, rendering therapies like Ventricular Tachycardia (VT) ablation ineffective. This case underlines the necessity for increased awareness and understanding of ARVD/C to aid in its early detection and management. Through such efforts, we aim to decrease morbidity and mortality associated with this challenging cardiac disorder.

Keywords: ARVD/C, cardiology, interventional cardiology, cardiac electrophysiology

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Authors: S. Tebibel, C. Mechati, S. Messaoudi

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Algeria is currently experiencing the same rate of cancer progression as that registered these last years in the western countries. Colorectal cancer, constituting increasingly a major public health problem, is the most common form of cancer after breast and Neck-womb cancer at the woman and prostate cancer at the man. Our work is based on a retrospective study to determine the cases of colorectal cancer through eastern Algeria. Our goal is to carry out an epidemiological, histological and immune- histochemical study to investigate different techniques for the diagnosis of colorectal cancer and their interests and specific in detecting the disease. The study includes 110 patients (aged between 20 to 87 years) with colorectal cancer where the inclusions and exclusions criteria were established. In our study, colorectal cancer, expresses a male predominance, with a sex ratio of 1, 99 and the most affected age group is between 50 and 59 years. We noted that the colon cancer rate is higher than rectal cancer rate, whose frequencies are respectively 60,91 % and 39,09 %. In the series of colon cancer, the ADK lieberkunien is histological the most represented type, or 85,07 % of all cases. In contrast, the proportion of ADK mucinous (colloid mucous) is only 1,49% only. Well-differentiated ADKS, are very significant in our series, they represent 83,58 % of cases. Adenocarcinoma moderately and poorly differentiated, whose proportions are respectively 2,99 % and 0.05 %. For histological varieties of rectal ADK, we see in our workforce that ADK lieberkunien represent the most common histological form, or 76,74%, while the mucosal colloid is 13,95 %. Research of the mutation on the gene encoding K-ras, a major step in the targeted therapy of colorectal cancers, is underway in our study. Colorectal cancer is the subject of much promising research concern: the evaluation of new therapies (antiangiogenic monoclonal antibodies), the search for predictors of sensitivity to chemotherapy and new prognostic markers using techniques of molecular biology and proteomics.

Keywords: adenocarcinoma, age, colorectal cancer, epidemiology, histological section, sex

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Authors: Rozeena Shaikh, Syed M Shahid, Jamil Ahmad, Qaisar Mansoor, Muhammad Ismail, Abid Azhar

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Introduction: Diabetes mellitus (DM) is a prevalent non-communicable disease worldwide. In most high-income countries as well as middle-income and low- income countries. DM is among the top causes of deaths. DM may lead to many vascular complications like hypertension, nephropathy, retinopathy, neuropathy, and foot. Diabetic nephropathy (DN) characterized by persistent albuminuria is a leading cause of end stage renal failure (ESRF). Pathogenesis of diabetic nephropathy is implicated by the polymorphisms in genes encoding the components of reninangiotensin- aldosteron system (RAAS) which include angiotensinogen (AGT), angiotensin-II receptor and particularly angiotensin converting enzyme (ACE) gene. Method: Study subjects include 110 control, 110 patients with DM without hypertension, 110 patients with DM with hypertension and 110 patients with DN. Blood samples were collected for Biochemical analysis and PCR and sequencing for the specific region of both genes. Results: The frequency of DD genotype and D allele of ACE (I/D) was significantly (p<0.05) high in DM normotensive, DM hypertensive and DN patients when compared to control. The ACE G2350A genotypes and allele frequencies were significantly different (p<0.05) in DM hypertensive patients as compared to control and DN, while no difference was observed between DM normotensive and DN when compared to control. The genotypes and alleles of AGT (M268T) polymorphism were significantly different (p<0.05) in DM normotensive, DM hypertensive and DN when compared to control. Conclusion: The DD genotype and D allele of ACE (I/D), GG genotype and G allele of ACE (G2350A) and the TT genotype and T allele of AGT (M268T) polymorphism have shown a significant difference in genotype and allele frequencies between controls and patients.

Keywords: genetic variations, ACE, AGT, diabetes mellitus, diabetic nephropathy, Pakistan

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Authors: Christina Killian, Katie Wall, Séamus Fanning, Guerrino Macori

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Deep-level metagenomics offers a useful technical approach to explore the three dynamic One Health axes: healthcare, domiciliary and veterinary. There is currently limited understanding of the composition of complex biofilms, natural abundance of AMR genes and gene transfer occurrence in these ecological niches. By using a newly established small-scale complex biofilm model, COMBAT has the potential to provide new information on microbial diversity, antimicrobial resistance (AMR)-encoding gene abundance, and their transfer in complex biofilms of importance to these three One Health axes. Shotgun metagenomics has been used to sample the genomes of all microbes comprising the complex communities found in each biofilm source. A comparative analysis between untreated and biocide-treated biofilms is described. The basic steps include the purification of genomic DNA, followed by library preparation, sequencing, and finally, data analysis. The use of long-read sequencing facilitates the completion of metagenome-assembled genomes (MAG). Samples were sequenced using a PromethION platform, and following quality checks, binning methods, and bespoke bioinformatics pipelines, we describe the recovery of individual MAGs to identify mobile gene elements (MGE) and the corresponding AMR genotypes that map to these structures. High-throughput sequencing strategies have been deployed to characterize these communities. Accurately defining the profiles of these niches is an essential step towards elucidating the impact of the microbiota on each niche biofilm environment and their evolution.

Keywords: COMBAT, biofilm, metagenomics, high-throughput sequencing

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Authors: Alina Goldberg Cavalleri, Sara Franco Ortega, Nawaporn Onkokesung, Richard Dale, Melissa Brazier-Hicks, Robert Edwards

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Non-target site based resistance (NTSR) to herbicides in weeds is a polygenic trait associated with the upregulation of proteins involved in xenobiotic detoxification and translocation we have termed the xenome. Among the xenome proteins, ABC transporters play a key role in enhancing herbicide metabolism by effluxing conjugated xenobiotics from the cytoplasm into the vacuole. The importance of ABC transporters is emphasized by the fact that they often contribute to multidrug resistance in human cells and antibiotic resistance in bacteria. They also play a key role in insecticide resistance in major vectors of human diseases and crop pests. By surveying available databases, transcripts encoding ABCs have been identified as being enhanced in populations exhibiting NTSR in several weed species. Based on a transcriptomics data in black grass (Alopecurus myosuroides, Am), we have identified three proteins from the ABC-C subfamily that are upregulated in NTSR populations. ABC-C transporters are poorly characterized proteins in plants, but in Arabidopsis localize to the vacuolar membrane and have functional roles in transporting glutathionylated (GSH)-xenobiotic conjugates. We found that the up-regulation of AmABCs strongly correlates with the up-regulation of a glutathione transferase termed AmGSTU2, which can conjugate GSH to herbicides. The expression profile of the ABC transcripts was profiled in populations of black grass showing different degree of resistance to herbicides. This, together with a phylogenetic analysis, revealed that AmABCs cluster in different groups which might indicate different substrate and roles in the herbicide resistance phenotype in the different populations

Keywords: black grass, herbicide, resistance, transporters

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Authors: José Eduardo García-Mendiola

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In this work, a phenomenological approach to computational modeling of analogy processing is carried out. The paper goes through the consideration of the structure of the analogy, based on the possibility of sustaining the genesis of its elements regarding Husserl's genetic theory of association. Among particular processes which take place in order to get analogical inferences, there is one which arises crucial for enabling efficient base cases retrieval through long-term memory, namely analogical transference grounded on familiarity. In general, it has been argued that analogical reasoning is a way by which a conscious agent tries to determine or define a certain scope of objects and relationships between them using previous knowledge of other familiar domain of objects and relations. However, looking for a complete description of analogy process, a deeper consideration of phenomenological nature is required in so far, its simulation by computational programs is aimed. Also, one would get an idea of how complex it would be to have a fully computational account of the analogy elements. In fact, familiarity is not a result of a mere chain of repetitions of objects or events but generated insofar as the object/attribute or event in question is integrable inside a certain context that is taking shape as functionalities and functional approaches or perspectives of the object are being defined. Its familiarity is generated not by the identification of its parts or objective determinations as if they were isolated from those functionalities and approaches. Rather, at the core of such a familiarity between entities of different kinds lays the way they are functionally encoded. So, and hoping to make deeper inroads towards these topics, this essay allows us to consider that cognitive-computational perspectives can visualize, from the phenomenological projection of the analogy process reviewing achievements already obtained as well as exploration of new theoretical-experimental configurations towards implementation of analogy models in specific as well as in general purpose machines.

Keywords: analogy, association, encoding, retrieval

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Authors: George Mahalu

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The Chua diode has been configured over time in various ways, using electronic structures like as operational amplifiers (OAs) or devices with gas or semiconductors. When discussing the use of semiconductor devices, tunnel diodes (Esaki diodes) are most often considered, and more recently, transistorized configurations such as lambda diodes. The paper-work proposed here uses in the modeling a lambda diode type configuration consisting of two Junction Field Effect Transistors (JFET). The original scheme is created in the MULTISIM electronic simulation environment and is analyzed in order to identify the conditions for the appearance of evolutionary unpredictability specific to nonlinear dynamic systems with chaos-induced behavior. The chaotic deterministic oscillator is one autonomous type, a fact that places it in the class of Chua’s type oscillators, the only significant and most important difference being the presence of a nonlinear device like the one mentioned structure above. The chaotic behavior is identified both by means of strange attractor-type trajectories and visible during the simulation and by highlighting the hypersensitivity of the system to small variations of one of the input parameters. The results obtained through simulation and the conclusions drawn are useful in the further research of ways to implement such constructive electronic solutions in theoretical and practical applications related to modern small signal amplification structures, to systems for encoding and decoding messages through various modern ways of communication, as well as new structures that can be imagined both in modern neural networks and in those for the physical implementation of some requirements imposed by current research with the aim of obtaining practically usable solutions in quantum computing and quantum computers.

Keywords: chaos, lambda diode, strange attractor, nonlinear system

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Authors: Tahani Aljohani, Jialin Yu, Alexandra. I. Cristea

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The more an educational system knows about a learner, the more personalised interaction it can provide, which leads to better learning. However, asking a learner directly is potentially disruptive, and often ignored by learners. Especially in the booming realm of MOOC Massive Online Learning platforms, only a very low percentage of users disclose demographic information about themselves. Thus, in this paper, we aim to predict learners’ demographic characteristics, by proposing an approach using linguistically motivated Deep Learning Architectures for Learner Profiling, particularly targeting gender prediction on a FutureLearn MOOC platform. Additionally, we tackle here the difficult problem of predicting the gender of learners based on their comments only – which are often available across MOOCs. The most common current approaches to text classification use the Long Short-Term Memory (LSTM) model, considering sentences as sequences. However, human language also has structures. In this research, rather than considering sentences as plain sequences, we hypothesise that higher semantic - and syntactic level sentence processing based on linguistics will render a richer representation. We thus evaluate, the traditional LSTM versus other bleeding edge models, which take into account syntactic structure, such as tree-structured LSTM, Stack-augmented Parser-Interpreter Neural Network (SPINN) and the Structure-Aware Tag Augmented model (SATA). Additionally, we explore using different word-level encoding functions. We have implemented these methods on Our MOOC dataset, which is the most performant one comparing with a public dataset on sentiment analysis that is further used as a cross-examining for the models' results.

Keywords: deep learning, data mining, gender predication, MOOCs

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Authors: Sushil Pradhan

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Biotechnology contributes to sustainable development in several ways such as biofertilizer production, biopesticide production and management of environmental pollution, tissue culture and biodiversity conservation in vitro, in vivo and in situ, Insectivorous medicinal plant Drosera burmannii Vahl belongs to the Family-Droseraceae under Order-Caryophyllales, Dicotyledoneae, Angiospermeae which has 31 (thirty one) living genera and 194 species besides 7 (seven) extinct (fossil) genera. Locally it is known as “Patkanduri” in Odia. Its Hindi name is “Mukhajali” and its English name is “Sundew”. The earliest species of Drosera was first reported in 1753 by Carolous Linnaeus called Drosera indica L (Indian Sundew). The latest species of Drosera reported by Fleisch A, Robinson, AS, McPherson S, Heinrich V, Gironella E and Madulida D.A. (2011) is Drosera ultramafica from Malaysia. More than 50 % species of Drosera have been reported from Australia and next to Australia is South Africa. India harbours only 3 species such as D. indica L, Drosera burmannii Vahl and D. peltata L. From our Odisha only D. burmannii Vahl is being reported for the first time from the district of Subarnapur near Sonepur (Arjunpur Reserve Forest Area). Drosera plant is autotrophic but to supplement its Nitrogen (N2) requirement it adopts heterotrophic mode of nutrition (insectivorous/carnivorous) as well. The colour of plant in mostly red and about 20-30cm in height with beautiful pink or white pentamerous flowers. Plants grow luxuriantly during November to February in shady and moist places near small water bodies of running water stream. Medicinally it is a popular herb in the locality for the treatment of cold and cough in children in rainy season by the local Doctors (Kabiraj and Baidya). In the present field investigation an attempt has been made to understand the unique reproductive phase and life cycle of the plant thereby planning for its conservation and propagation through various techniques of tissue culture and biotechnology. More importantly besides morphological and anatomical studies, cytological investigation is being carried out to find out the number of chromosomes in the cell and its genomics as there is no such report as yet for Drosera burmannii Vahl. The ecological significance and biodiversity conservation of Drosera with special reference to energy, environmental and chemical engineering has been discussed in the research paper presentation.

Keywords: insectivorous, medicinal, drosera, biotechnology, chromosome, genome

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Authors: Isaac K. E. Ampomah, Seong-Bae Park, Sang-Jo Lee

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Over the past decade, there have been promising developments in Natural Language Processing (NLP) with several investigations of approaches focusing on Recognizing Textual Entailment (RTE). These models include models based on lexical similarities, models based on formal reasoning, and most recently deep neural models. In this paper, we present a sentence encoding model that exploits the sentence-to-sentence relation information for RTE. In terms of sentence modeling, Convolutional neural network (CNN) and recurrent neural networks (RNNs) adopt different approaches. RNNs are known to be well suited for sequence modeling, whilst CNN is suited for the extraction of n-gram features through the filters and can learn ranges of relations via the pooling mechanism. We combine the strength of RNN and CNN as stated above to present a unified model for the RTE task. Our model basically combines relation vectors computed from the phrasal representation of each sentence and final encoded sentence representations. Firstly, we pass each sentence through a convolutional layer to extract a sequence of higher-level phrase representation for each sentence from which the first relation vector is computed. Secondly, the phrasal representation of each sentence from the convolutional layer is fed into a Bidirectional Long Short Term Memory (Bi-LSTM) to obtain the final sentence representations from which a second relation vector is computed. The relations vectors are combined and then used in then used in the same fashion as attention mechanism over the Bi-LSTM outputs to yield the final sentence representations for the classification. Experiment on the Stanford Natural Language Inference (SNLI) corpus suggests that this is a promising technique for RTE.

Keywords: deep neural models, natural language inference, recognizing textual entailment (RTE), sentence-to-sentence relation

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Authors: Sangyeop Shin, D. C. M. Kulatunga, S. H. S. Dananjaya, Chamilani Nikapitiya, Jehee Lee, Mahanama De Zoysa

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Saprolegniasis is one of the most devastating fungal diseases in freshwater fish which is caused by species in the genus Saprolegnia including Saprolegnia parasitica. In this study, we isolated the strain of S. parasitica from diseased rainbow trout in Korea. Morphological and molecular based identification confirmed that isolated fungi belong to the member of S. parasitica, supported by its typical fungal features including cotton-like whitish mycelium, zoospores (primary and secondary) and phylogenetic analysis with internal transcribed spacer (ITS) region. Pathogenicity of isolated S. parasitica was developed in embryo, larvae, juvenile and adult zebrafish as a disease model. Up regulation of host genes encoding ZfTnf-α, Zfc-Rel, ZfIl-12, ZfLyz-c, Zfβ-def, and ZfHsp-70 was identified in zebrafish larvae after experimental challenge of S. parasitica showing the host immune responses against the S. parasitica. Survival of the juveniles upon fungal infection might be due to the increased immune protection in the host. Investigation of antifungal susceptibility of S. parasitica with natural lawsone (2-hydroxy-1,4-naphthoquinone) revealed the minimum inhibitory concentration (MIC) and percentage inhibition of radial growth (PIRG %) as 200 µg/mL and 31.8%, respectively. Lawsone was able to change the membrane permeability, and cause irreversible damage and disintegration to the cellular membranes of S. parasitica which might have effect on fungi growth inhibition. Moreover, the mycelium exposed to lawsone (MIC level) changed the transcriptional responses of S. parasitica genes. Overall results indicate that lawsone could be a potential and novel anti-S. parasitica agent for controlling S. parasitica infection.

Keywords: host-pathogen interactions, lawsone, rainbow trout, Saprolegnia parasitica, Saprolegniasis, zebrafish

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Authors: Juliana Lukša, Bazilė Ravoitytė, Elena Servienė, Saulius Serva

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Totiviridae L-A virus is a persistent Saccharomyces cerevisiae dsRNA virus. It encodes the major structural capsid protein Gag and Gag-Pol fusion protein, responsible for virus replication and encapsulation. These features also enable the copying of satellite dsRNAs (called M dsRNAs) encoding a secreted toxin and immunity to it (known as killer toxin). Viral capsid pore presumably functions in nucleotide uptake and viral mRNA release. During cell division, sporogenesis, and cell fusion, the virions remain intracellular and are transferred to daughter cells. By employing high throughput RNA sequencing data analysis, we describe the influence of solely L-A virus on the expression of genes in three different S. cerevisiae hosts. We provide a new perception into Totiviridae L-A virus-related transcriptional regulation, encompassing multiple bioinformatics analyses. Transcriptional responses to L-A infection were similar to those induced upon stress or availability of nutrients. It also delves into the connection between the cell metabolism and L-A virus-conferred demands to the host transcriptome by uncovering host proteins that may be associated with intact virions. To better understand the virus-host interaction, we applied differential proteomic analysis of virus particle-enriched fractions of yeast strains that harboreither complete killer system (L-A-lus and M-2 virus), M-2 depleted orvirus-free. Our analysis resulted in the identification of host proteins, associated with structural proteins of the virus (Gag and Gag-Pol). This research was funded by the European Social Fund under the No.09.3.3-LMT-K-712-19-0157“Development of Competences of Scientists, other Researchers, and Students through Practical Research Activities” measure.

Keywords: totiviridae, killer virus, proteomics, transcriptomics

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Authors: Irene Alevizos, Jessica Lewis, Marina Harper, John Boyce

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Acinetobacter baumannii causes a range of severe nosocomial-acquired infections, and many strains are multi-drug resistant. A. baumannii possesses survival mechanisms allowing it to thrive in competitive polymicrobial environments, including a Type VI Secretion System (T6SS) that injects effector proteins into other bacteria to give a competitive advantage. The effects of T6SS firing are broad and depend entirely on the effector that is delivered. Effects can include toxicity against prokaryotic or eukaryotic cells and the acquisition of essential nutrients. The T6SS of some species can deliver ‘specialised effectors’ that are fused directly to T6SS components, such as PAAR proteins. PAAR proteins are predicted to form the piercing tip of the T6SS and are essential for T6SS function. Although no specialised effectors have been identified in A. baumannii, many strains encode multiple PAAR proteins. Analysis of PAAR proteins across the species identified 12 families of PAAR proteins with distinct C-terminal extensions. A. baumannii AB307-0294 encodes two PAAR proteins, one of which has a C-terminal extension. Mutation of one or both of the PAAR-encoding genes in this strain showed that expression of either PAAR protein was sufficient for T6SS function. We employed a heterologous expression approach and determined that PAAR proteins from different A. baumannii strains, as well as the closely related A. baylyi species, could complement the A. baumannii ∆paar mutant and restore T6SS function. Furthermore, we showed that PAAR fusions could be used to deliver artificially cloned protein fragments by generating Histidine- and Streptavidin- tagged PAAR specialised effectors, which restored T6SS activity. This provides evidence that the fusion of protein fragments onto PAAR proteins in A. baumannii is compatible with a functional T6SS. Successful delivery by this mechanism extends the scope of what the T6SS can deliver, including user designed proteins.

Keywords: A. baumannii, effectors, PAAR, T6SS

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Authors: Chutamas Thepmalee, Aussara Panya, Mutita Junking, Jatuporn Sujjitjoon, Nunghathai Sawasdee, Pa-Thai Yenchitsomanus

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Cholangiocarcinoma (CCA) is an aggressive malignancy of bile duct epithelial cells in which the standard treatments, including surgery, radiotherapy, chemotherapy, and targeted therapy are partially effective. Many solid tumors including CCA escape host immune responses by creating tumor microenvironment and generating immunosuppressive cytokines such as interleukin-10 (IL-10) and transforming growth factor-β (TGF-β). These cytokines can inhibit dendritic cell (DC) differentiation and function, leading to decreased activation and response of effector CD4+ and CD8+ T cells for cancer cell elimination. To overcome the effects of these immunosuppressive cytokines and to increase ability of DC to activate effector CD4+ and CD8+ T cells, we generated self-differentiated DCs (SD-DCs) with down-regulation of IL-10 and TGF-β receptors for activation of effector CD4+ and CD8+ T cells. Human peripheral blood monocytes were initially transduced with lentiviral particles containing the genes encoding GM-CSF and IL-4 and then secondly transduced with lentiviral particles containing short-hairpin RNAs (shRNAs) to knock-down mRNAs of IL-10 and TGF-β receptors. The generated SD-DCs showed up-regulation of MHC class II (HLA-DR) and co-stimulatory molecules (CD40 and CD86), comparable to those of DCs generated by convention method. Suppression of IL-10 and TGF-β receptors on SD-DCs by specific shRNAs significantly increased levels of IFN-γ and also increased cytolytic activity of DC-activated effector T cells against CCA cell lines (KKU-213 and KKU-100), but it had little effect to immortalized cholangiocytes (MMNK-1). Thus, SD-DCs with down-regulation of IL-10 and TGF-β receptors increased activation of effector T cells, which is a recommended method to improve DC function for the preparation of DC-activated effector T cells for adoptive T-cell therapy.

Keywords: cholangiocarcinoma, IL-10 receptor, self-differentiated dendritic cells, TGF-β receptor

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Authors: Iman Kamranfar, Gang-Ping Xue, Salma Balazadeh, Bernd Mueller-Roeber

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Adverse environmental conditions such as salinity stress, high temperature and drought limit plant growth and typically lead to precocious tissue degeneration and leaf senescence, a process by which nutrients from photosynthetic organs are recycled for the formation of flowers and seeds to secure reaching the next generation under such harmful conditions. In addition, abiotic stress affects developmental patterns that help the plant to withstand unfavourable environmental conditions. We discovered an NAC (for NAM, ATAF1, 2, and CUC2) transcription factor (TF), called RAF in the following, which plays a central role in abiotic drought stress-triggered senescence and the control of developmental adaptations to stressful environments. RAF is an ABA-responsive TF; RAF overexpressors are hypersensitive to abscisic acid (ABA) and exhibit precocious senescence while knock-out mutants show delayed senescence. To explore the RAF gene regulatory network (GRN), we determined its preferred DNA binding sites by binding site selection assay (BSSA) and performed microarray-based expression profiling using inducible RAF overexpression lines and chromatin immunoprecipitation (ChIP)-PCR. Our studies identified several direct target genes, including those encoding for catabolic enzymes acting during stress-induced senescence. Furthermore, we identified various genes controlling drought stress-related developmental changes. Based on our results, we conclude that RAF functions as a central transcriptional regulator that coordinates developmental programs with stress-related inputs from the environment. To explore the potential agricultural applications of our findings, we are currently extending our studies towards crop species.

Keywords: abiotic stress, Arabidopsis, development, transcription factor

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Authors: Atsuko Okazaki, Jurg Ott

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Some genetic diseases (‘digenic traits’) are due to the interaction between two DNA variants. For example, certain forms of Retinitis Pigmentosa (a genetic form of blindness) occur in the presence of two mutant variants, one in the ROM1 gene and one in the RDS gene, while the occurrence of only one of these mutant variants leads to a completely normal phenotype. Detecting such digenic traits by genetic methods is difficult. A common approach to finding disease-causing variants is to compare 100,000s of variants between individuals with a trait (cases) and those without the trait (controls). Such genome-wide association studies (GWASs) have been very successful but hinge on genetic effects of single variants, that is, there should be a difference in allele or genotype frequencies between cases and controls at a disease-causing variant. Frequent pattern mining (FPM) methods offer an avenue at detecting digenic traits even in the absence of single-variant effects. The idea is to enumerate pairs of genotypes (genotype patterns) with each of the two genotypes originating from different variants that may be located at very different genomic positions. What is needed is for genotype patterns to be significantly more common in cases than in controls. Let Y = 2 refer to cases and Y = 1 to controls, with X denoting a specific genotype pattern. We are seeking association rules, ‘X → Y’, with high confidence, P(Y = 2|X), significantly higher than the proportion of cases, P(Y = 2) in the study. Clearly, generally available FPM methods are very suitable for detecting disease-associated genotype patterns. We use fpgrowth as the basic FPM algorithm and built a framework around it to enumerate high-frequency digenic genotype patterns and to evaluate their statistical significance by permutation analysis. Application to a published dataset on opioid dependence furnished results that could not be found with classical GWAS methodology. There were 143 cases and 153 healthy controls, each genotyped for 82 variants in eight genes of the opioid system. The aim was to find out whether any of these variants were disease-associated. The single-variant analysis did not lead to significant results. Application of our FPM implementation resulted in one significant (p < 0.01) genotype pattern with both genotypes in the pattern being heterozygous and originating from two variants on different chromosomes. This pattern occurred in 14 cases and none of the controls. Thus, the pattern seems quite specific to this form of substance abuse and is also rather predictive of disease. An algorithm called Multifactor Dimension Reduction (MDR) was developed some 20 years ago and has been in use in human genetics ever since. This and our algorithms share some similar properties, but they are also very different in other respects. The main difference seems to be that our algorithm focuses on patterns of genotypes while the main object of inference in MDR is the 3 × 3 table of genotypes at two variants.

Keywords: digenic traits, DNA variants, epistasis, statistical genetics

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Authors: Thanusha D. Abeywickrama, Inoka C. Perera, Genji Kurisu

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Tuberculosis, considered being as the ninth leading cause of death worldwide, cause from a single infectious agent M. tuberculosis and the drug resistance nature of this bacterium is a continuing threat to the world. Therefore TB preventing treatment is expanding, where this study designed to analyze the regulatory mechanism of GntR transcriptional regulator gene Rv0792c, which lie between several genes codes for some hypothetical proteins, a monooxygenase and an oxidoreductase. The gene encoding Rv0792c was cloned into pET28a and expressed protein was purified to near homogeneity by Nickel affinity chromatography. It was previously reported that the protein binds within the intergenic region (BS region) between Rv0792c gene and monooxygenase (Rv0793). This resulted in binding of three protein molecules with the BS region suggesting tight control of monooxygenase as well as its own gene. Since monooxygenase plays a key role in metabolism, this gene may have a global regulatory role. The natural ligand for this regulator is still under investigation. In relation to the Rv0792 protein structure, a Circular Dichroism (CD) spectrum was carried out to determine its secondary structure elements. Percentage-wise, 17.4% Helix, 21.8% Antiparallel, 5.1% Parallel, 12.3% turn and 43.5% other were revealed from CD spectrum data under room temperature. Differential Scanning Calorimetry (DSC) was conducted to assess the thermal stability of Rv0792, which the melting temperature of protein is 57.2 ± 0.6 °C. The graph of heat capacity (Cp) versus temperature for the best fit was obtained for non-two-state model, which concludes the folding of Rv0792 protein occurs through stable intermediates. Peak area (∆HCal ) and Peak shape (∆HVant ) was calculated from the graph and ∆HCal / ∆HVant was close to 0.5, suggesting dimeric nature of the protein.

Keywords: CD spectrum, DSC analysis, GntR transcriptional regulator, protein structure

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Authors: Tarik Sipahi

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Photonics research continues to push the boundaries of optical science, and the development of metasurface technology has emerged as a transformative force in this domain. The work presents the intricacies of a unified metasurface design tailored for efficient polarization and color control in optical systems. The proposed unified metasurface serves as a singular, nanoengineered optical element capable of simultaneous polarization modulation and color encoding. Leveraging principles from metamaterials and nanophotonics, this design allows for unprecedented control over the behavior of light at the subwavelength scale. The metasurface's spatially varying architecture enables seamless manipulation of both polarization states and color wavelengths, paving the way for a paradigm shift in optical system design. The advantages of this unified metasurface are diverse and impactful. By consolidating functions that traditionally require multiple optical components, the design streamlines optical systems, reducing complexity and enhancing overall efficiency. This approach is particularly promising for applications where compactness, weight considerations, and multifunctionality are crucial. Furthermore, the proposed unified metasurface design not only enhances multifunctionality but also addresses key challenges in optical system design, offering a versatile solution for applications demanding compactness and lightweight structures. The metasurface's capability to simultaneously manipulate polarization and color opens new possibilities in diverse technological fields. The research contributes to the evolution of optical science by showcasing the transformative potential of metasurface technology, emphasizing its role in reshaping the landscape of optical system architectures. This work represents a significant step forward in the ongoing pursuit of pushing the boundaries of photonics, providing a foundation for future innovations in compact and efficient optical devices.

Keywords: metasurface, nanophotonics, optical system design, polarization control

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Authors: Satendra Pal Singh, Dalip Kr. Kakru, Jyoti Mishra, Rajesh Thakur, Tarana Sarwat

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COVID-19 is still an intrigue as far as morbidity or mortality is concerned. The rate of recovery varies from person to person, & it depends upon the accessibility of the healthcare system and the roles played by the physicians and caregivers. It is envisaged that with the passage of time, people would become immune to this virus, and those who are vulnerable would sustain themselves with the help of vaccines. The proposed study deals with the severeness of COVID-19 is associated with some specific biomarkers linked to correlate age and gender. We will be assessing the overall homeostasis of the persons who were affected by the coronavirus infection and also of those who recovered from it. Some people show more severe effects, while others show very mild symptoms, however, they show low CT values. Thus far, it is unclear why the new strain of Covid has different effects on different people in terms of age, gender, and ABO blood typing. According to data, the fatality rate with heart disease was 10.5 percent, 7.3 percent were diabetic, and 6 percent who are already infected from other comorbidities. However, some COVID-19 cases are worse than others & it is not fully explainable as of date. Overall data show that the ABO blood group is effective or prone to the risk of SARS-COV2 infection, while another study also shows the phenotypic effects of the blood group related to covid. It is an accepted fact that females have more strong immune systems than males, which may be related to the fact that females have two ‘X’ chromosomes, which might contain a more effective immunity booster gene on the X chromosome, and are capable to protect the female. Also specific sex hormones also induce a better immune response in a specific gender. This calls for in-depth analysis to be able to gain insight into this dilemma. COVID-19 is still not fully characterized, and thus we are not very familiar with its biology, mode of infection, susceptibility, and overall viral load in the human body. How many virus particles are needed to infect a person? How, then, comorbidity contribute to coronavirus infection? Since the emergence of this virus in 2020, a large number of papers have been published, and seemingly, vaccines have been prepared. But still, a large number of questions remain unanswered. The proneness of humans for infection by covid-19 needs to be established to be able to develop a better strategy to fight this virus. Our study will be on the Impact of demography on the Severity of covid-19 infection & at the same time, will look into gender-specific sensitivity of Covid-19 and the Operational variation of different biochemical markers in Covid-19 positive patients. Besides, we will be studying the co-relation, if any, of COVID severity & ABO Blood group type and the occurrence of the most common blood group type amongst positive patience.

Keywords: coronavirus, ABO blood group, age, gender

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Authors: Tettey Afi Pamela, Sotaro Fujii, Hidetoshi Saito, Kawaii Koichiro

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Introduction: Organisms employ adaptive mechanisms when faced with any stressor or risk of being wiped out. This has made it possible for them to survive in harsh environmental conditions such as increasing temperature, low pH, and anoxia. Some of the mechanisms they utilize include the expression of heat shock proteins, synthesis of cryoprotectants, and anhydrobiosis. Heat shock proteins (HSPs) have been widely studied to determine their involvement in stress tolerance among various organism, of which chironomid species have been no exception. We examined the survival and expression of genes encoding five (5) heat shock proteins (HSP70, HSP67, HSP60, HSP27, and HSP23) from Chironomus sulfurosus larvae reared from 1st instar at 25°C, 30°C, 35°C, and 40°C. Results: The highest survival rate was recorded at 30°C, followed by 25°C, then 35°C. Only a small percentage of C. sulfurosus survived at 40°C (14.5%). With regards to HSPs expression, some HSPs responded to an increase in high temperature. The relative expression levels were lowest at 30°C for HSP70, HSP60, HSP27, and HSP23. At 25°C and 40°C, HSP70, HSP67, HSP60, HSP27, and HSP23 had the highest expression. At 35°C, all had the lowest expression. Discussion: The expression of heat shock proteins varies from one species to another. We designated the genes HSP 70, HSP 67, HSP 60, HSP 27, and HSP 23 genes based on transcriptome analysis of C. sulfurosus. Our study can be termed as a long-heat shock study as C. sulfurosus was reared from the first instar to the fourth instar, and this might have led to a continuous induction of HSPs at 25°C. 40°C had the lowest survival but highest HSPs expression as C. sulfurosus larvae had to utilize HSPs for sustenance. These results and future high-throughput studies at both the transcriptome and proteome level will improve the information needed to predict the future geographic distribution of these species within the context of global warming.

Keywords: chironomid, heat shock proteins, high temperature, heat shock protein expression

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Authors: D. López-Mancilla, J. M. Roblero-Villa

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Since 1990, the research on chaotic dynamics has received considerable attention, particularly in light of potential applications of this phenomenon in secure communications. Data encryption using chaotic systems was reported in the 90's as a new approach for signal encoding that differs from the conventional methods that use numerical algorithms as the encryption key. The algorithms for image encryption have received a lot of attention because of the need to find security on image transmission in real time over the internet and wireless networks. Known algorithms for image encryption, like the standard of data encryption (DES), have the drawback of low level of efficiency when the image is large. The encrypting based on chaos proposes a new and efficient way to get a fast and highly secure image encryption. In this work, a user interface for image encryption and a novel and easiest way to encrypt images using chaos are presented. The main idea is to reshape any image into a n-dimensional vector and combine it with vector extracted from a chaotic system, in such a way that the vector image can be hidden within the chaotic vector. Once this is done, an array is formed with the original dimensions of the image and turns again. An analysis of the security of encryption from the images using statistical analysis is made and is used a stage of optimization for image encryption security and, at the same time, the image can be accurately recovered. The user interface uses the algorithms designed for the encryption of images, allowing you to read an image from the hard drive or another external device. The user interface, encrypt the image allowing three modes of encryption. These modes are given by three different chaotic systems that the user can choose. Once encrypted image, is possible to observe the safety analysis and save it on the hard disk. The main results of this study show that this simple method of encryption, using the optimization stage, allows an encryption security, competitive with complicated encryption methods used in other works. In addition, the user interface allows encrypting image with chaos, and to submit it through any public communication channel, including internet.

Keywords: image encryption, chaos, secure communications, user interface

Procedia PDF Downloads 457

Authors: Virupakshi Hiremata, Ratnakar M. Shet, Raghavendra Gunnaiah, Prashantha A.

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Muskmelon is a health-beneficial and refreshing dessert vegetable with a low shelf life. Mangalore melon, a genetic homeologue of muskmelon, has a shelf life of more than six months and is mostly used for culinary purposes. Understanding the genetics of shelf life, yield and yield-related traits and identification of markers linked to such traits is helpful in transfer of extended shelf life from Mangalore melon to the muskmelon through intra-specific hybridization. For QTL mapping, 276 F2 mapping population derived from the cross Arka Siri × SS-17 was genotyped with 40 polymorphic markers distributed across 12 chromosomes. The same population was also phenotyped for yield, shelf life and fruit quality traits. One major QTL (R2 >10) and fourteen minor QTLs (R2 <10) localized on four linkage groups, governing different traits were mapped in F2 mapping population developed from the intraspecific cross with a LOD > 5.5. The phenotypic varience explained by each locus varied from 3.63 to 10.97 %. One QTL was linked to shelf-life (qSHL-3-1), five QTLs were linked to TSS (qTSS-1-1, qTSS-3-3, qTSS-3-1, qTSS-3-2 and qTSS-1-2), two QTLs for flesh thickness (qFT-3-1, and qFT-3-2) and seven QTLs for fruit yield per vine (qFYV-3-1, qFYV-1-1, qFYV-3-1, qFYV1-1, qFYV-1-3, qFYV2-1 and qFYV6-1). QTL flanking markers may be used for marker assisted introgression of shelf life into muskmelon. Important QTL will be further fine-mapped for identifying candidate genes by QTLseq and RNAseq analysis. Fine-mapping of Important Quantitative Trait Loci (QTL) holds immense promise in elucidating the genetic basis of complex traits. Leveraging advanced techniques like QTLseq and RNA sequencing (RNA seq) is crucial for this endeavor. QTLseq combines next-generation sequencing with traditional QTL mapping, enabling precise identification of genomic regions associated with traits of interest. Through high-throughput sequencing, QTLseq provides a detailed map of genetic variations linked to phenotypic variations, facilitating targeted investigations. Moreover, RNA seq analysis offers a comprehensive view of gene expression patterns in response to specific traits or conditions. By comparing transcriptomes between contrasting phenotypes, RNA seq aids in pinpointing candidate genes underlying QTL regions. Integrating QTLseq with RNA seq allows for a multi-dimensional approach, coupling genetic variation with gene expression dynamics.

Keywords: QTL, shelf life, TSS, muskmelon and Mangalore melon

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Authors: Rabih Joseph Nabhan

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This case study explores the impact of two major computer software programs Learn to Speak English and Learn English Spelling and Pronunciation, and some Internet search engines such as Google on mending the decoding and spelling deficiency of Simon X, a dyslexic student. The improvement in decoding and spelling may result in better reading comprehension and composition writing. Some computer programs and Internet materials can help regain the missing awareness and consequently restore his self-confidence and self-esteem. In addition, this study provides a systematic plan comprising a set of activities (four computer programs and Internet materials) which address the problem from the lowest to the highest levels of phoneme and phonological awareness. Four methods of data collection (accounts, observations, published tests, and interviews) create the triangulation to validly and reliably collect data before the plan, during the plan, and after the plan. The data collected are analyzed quantitatively and qualitatively. Sometimes the analysis is either quantitative or qualitative, and some other times a combination of both. Tables and figures are utilized to provide a clear and uncomplicated illustration of some data. The improvement in the decoding, spelling, reading comprehension, and composition writing skills that occurred is proved through the use of authentic materials performed by the student under study. Such materials are a comparison between two sample passages written by the learner before and after the plan, a genuine computer chat conversation, and the scores of the academic year that followed the execution of the plan. Based on these results, the researcher recommends further studies on other Lebanese dyslexic learners using the computer to mend their language problem in order to design and make a most reliable software program that can address this disability more efficiently and successfully.

Keywords: analysis, awareness, dyslexic, software

Procedia PDF Downloads 195

Authors: Abiodun Olayinka, Daniel Dzidzienyo, Pangirayi Tongoona, Samuel Offei, Edwige Gaby Nkouaya Mbanjo, Chiedozie Egesi, Ismail Yusuf Rabbi

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Cassava (Manihot esculenta Crantz) is a major source of starch for various industrial applications. However, the traditional cultivation and harvesting methods of cassava are labour-intensive and inefficient, limiting the supply of fresh cassava roots for industrial starch production. To achieve improved productivity and quality of fresh cassava roots through mechanized cultivation, cassava cultivars with compact plant architecture and moderate plant height are needed. Plant architecture-related traits, such as plant height, harvest index, stem diameter, branching angle, and lodging tolerance, are critical for crop productivity and suitability for mechanized cultivation. However, the genetics of cassava plant architecture remain poorly understood. This study aimed to identify the genetic bases of the relationships between plant architecture traits and productivity-related traits, particularly starch content. A panel of 453 clones developed at the International Institute of Tropical Agriculture, Nigeria, was genotyped and phenotyped for 18 plant architecture and productivity-related traits at four locations in Nigeria. A genome-wide association study (GWAS) was conducted using the phenotypic data from a panel of 453 clones and 61,238 high-quality Diversity Arrays Technology sequencing (DArTseq) derived Single Nucleotide Polymorphism (SNP) markers that are evenly distributed across the cassava genome. Five significant associations between ten SNPs and three plant architecture component traits were identified through GWAS. We found five SNPs on chromosomes 6 and 16 that were significantly associated with shoot weight, harvest index, and total yield through genome-wide association mapping. We also discovered an essential candidate gene that is co-located with peak SNPs linked to these traits in M. esculenta. A review of the cassava reference genome v7.1 revealed that the SNP on chromosome 6 is in proximity to Manes.06G101600.1, a gene that regulates endodermal differentiation and root development in plants. The findings of this study provide insights into the genetic basis of plant architecture and yield in cassava. Cassava breeders could leverage this knowledge to optimize plant architecture and yield in cassava through marker-assisted selection and targeted manipulation of the candidate gene.

Keywords: Manihot esculenta Crantz, plant architecture, DArtseq, SNP markers, genome-wide association study

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Authors: Dhanya Nair, Nicholas Mirchandani

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Musical haptic systems can enhance a listener’s musical experience while providing an alternative platform for the hearing impaired to experience music. Current music tactile technologies focus on representing tactile metronomes to synchronize performers or encoding musical notes into distinguishable (albeit distracting) tactile patterns. There is growing interest in the development of musical haptic systems to augment the auditory experience, although the haptic-music relationship is still not well understood. This paper represents a tactile music interface that provides vibrations to multiple fingertips in synchronicity with auditory music. Like an audio equalizer, different frequency bands are filtered out, and the power in each frequency band is computed and converted to a corresponding vibrational strength. These vibrations are felt on different fingertips, each corresponding to a different frequency band. Songs with music from different spectrums, as classified by their energy and valence, were used to test the effectiveness of the system and to understand the relationship between music and tactile sensations. Three participants were trained on one song categorized as sad (low energy and low valence score) and one song categorized as happy (high energy and high valence score). They were trained both with and without auditory feedback (listening to the song while experiencing the tactile music on their fingertips and then experiencing the vibrations alone without the music). The participants were then tested on three songs from both categories, without any auditory feedback, and were asked to classify the tactile vibrations they felt into either category. The participants were blinded to the songs being tested and were not provided any feedback on the accuracy of their classification. These participants were able to classify the music with 100% accuracy. Although the songs tested were on two opposite spectrums (sad/happy), the preliminary results show the potential of utilizing a vibrotactile equalizer, like the one presented, for augmenting musical experience while furthering the current understanding of music tactile relationship.

Keywords: haptic music relationship, tactile equalizer, tactile music, vibrations and mood

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Authors: N. Umasuthan, S. D. N. K. Bathige, W. S. Thulasitha, I. Whang, J. Lee

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The MyD88 is an evolutionarily conserved host-expressed adaptor protein that is essential for proper TLR/ IL1R immune-response signaling. A previously identified complete cDNA (1626 bp) of OfMyD88 comprised an ORF of 867 bp encoding a protein of 288 amino acids (32.9 kDa). The gDNA (3761 bp) of OfMyD88 revealed a quinquepartite genome organization composed of 5 exons (with the sizes of 310, 132, 178, 92 and 155 bp) separated by 4 introns. All the introns displayed splice signals consistent with the consensus GT/AG rule. A bipartite domain structure with two domains namely death domain (24-103) coded by 1st exon, and TIR domain (151-288) coded by last 3 exons were identified through in silico analysis. Moreover, homology modeling of these two domains revealed a similar quaternary folding nature between human and rock bream homologs. A comprehensive comparison of vertebrate MyD88 genes showed that they possess a 5-exonic structure. In this structure, the last three exons were strongly conserved, and this suggests that a rigid structure has been maintained during vertebrate evolution. A cluster of TATA box-like sequences were found 0.25 kb upstream of cDNA starting position. In addition, putative 5'-flanking region of OfMyD88 was predicted to have TFBS implicated with TLR signaling, including copies of NFB1, APRF/ STAT3, Sp1, IRF1 and 2 and Stat1/2. Using qPCR technique, a ubiquitous mRNA expression was detected in liver and blood. Furthermore, a significantly up-regulated transcriptional expression of OfMyD88 was detected in head kidney (12-24 h; >2-fold), spleen (6 h; 1.5-fold), liver (3 h; 1.9-fold) and intestine (24 h; ~2-fold) post-Fla challenge. These data suggest a crucial role for MyD88 in antibacterial immunity of teleosts.

Keywords: MyD88, innate immunity, flagellin, genomic analysis

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