Transcriptomic Profiling Using Next Generation Sequencing - Advances, Advantages, and Challenges

Transcriptome, the functional element of the genome, is comprised of different kinds of RNA molecules such as mRNA, miRNA, ncRNA, rRNA, and tRNA to name a few. Each of these RNA molecules plays a vital role in the physiological response, and understanding the regulation of these molecules is extremely critical for the better understanding of the functional genome. RNA Sequencing (RNASeq) is one of the latest techniques applied to study genome-wide transcriptome characterization and profiling using high-throughput sequenced data. As compared to array-based methods, RNASeq provides in-depth and more precise information on transcriptome characterization and quantification. Based upon availability of reference genome, transcriptome assembly can be reference-guided or de novo. Once transcripts are assembled, downstream analysis such as expression profiling, gene ontology, and pathway enrichment analyses can give more insight into gene regulation. This chapter describes the significance of RNASeq study over array-based traditional methods, approach to analyze RNASeq data, available methods and tools, challenges associated with the data analysis, application areas, some of the recent advancement made in the area of transcriptome study and its application

Optimization of thermoelectric cooling technology for an active cooling of photovoltaic panel

The electrical efficiency of PV panel is undesirably influenced by the rise in the panel temperature and accelerates cell degradation which leads to reduction of life expectancy of PV module. A fall in PV module output power with rise in temperature is observed on non-removal of this excessive heat. For cooling such system, thermoelectric technology is appropriate for its integration adjacent to the PV module. Thermoelectric module (TEM) is attached at the back side of PV module for absorption of the heat generated in PV module by infrared spectrum. This paper deals with the active heat sinking from PV system using TEM tiles. Mathematical model for TEM is developed by consideration of temperature dependence of material properties. A temperature based maximum power point tracking (MPPT) scheme is presented for operating TEM at optimal temperature of PV system. Analysis and design of MPPT scheme, current controller and converter are also discussed. The performance improvement of PV system with thermoelectric cooling is presented through simulated results under MATLAB environment to compute the adequate heat sinking from the PV system exposed to wide spectrum other than visible light

To Study the Microbiological Flora in Chronic SuppurativeOttis Media At Tertiary Care Center

Introduction: Indiscriminate use of antibiotics multi-drug resistant bacterial strains has increased disease complications. Changes in bacterial flora seen in the last decade which has been verified by various authors.Knowledge of the causative organisms and their antibiotic sensitivity is important in deciding the medical management of both safe and unsafe types of CSOM.Materials and method: It’s a descriptive prospective observational type of study conducted at department of ENT and head & neck surgery, A.B.V Government Medical College, Vidisha, M.P, India it is a tertiary care center. The duration of study was 1 year from April 2018- May 2019; 100 patients were included in the study,Observation and results: In our study we have taken samples from 100 patients, 65 patients (65%) had tubotympanic type while 35 patients (35%) had atticoantral type of CSOM. Microbial growth was obtained in 85 (85%) samples, 15 had no growth (15%) being mono-microbial in 81 (81%) while mixed growth was obtained in 4 (4%) samples. P. aeruginosa (32.30%) and S. aureus was most common isolates in patients with tubotympanic CSOM.In atticoantral type of CSOM most common isolates were P. aeruginosa (42.82%) followed by S.aureus Fungal positivity was observed in 06 (9.23%) cases of tubotympanic CSOM only

Epidemiological and mycological characteristics of candidemia in patients with hematological malignancies attending a tertiary-care center in India

Background and objectives: We undertook the present study to ascertain the contributing risk factors and explore the epidemiological and mycological characteristics of opportunistic candidemia among patients with hematological malignancies. Design and settings: Observational cross-sectional study in a tertiary care center. Patients and methods: Consecutive patients with hematological malignancies reporting to the collaborating medical and pediatric units with a febrile episode were recruited and screened for candidemia by blood culture. Recovered Candida isolates were speciated and antifungal susceptibility testing was performed as per Clinical and Laboratory Standards Institute guideline (CLSI) guidelines M44-A. Further analysis was done for potential risk factors and compared between culture positive and negative patients. Results: Of 150 patients recruited, the majority (n = 27) were between 51 and 60 years and the male to female ratio was 1.63:1. Fifteen patients (10%) were culture positive. The culture positivity was significantly higher in acute lymphocytic leukemia (ALL) than in non-ALL patients (p = 0.03). There was significant association of candidaemia with leucopenia, chemotherapeutic drugs, corticosteroids and presence of indwelling devices. Duration of disease (p = 0.032) and duration of hospitalization (p = 0.003) were significantly prolonged in culture positive patients. C. tropicalis was the commonest isolate (46.67%), with non- Candida albicans outnumbering C. albicans in all categories of hematological malignancies (2.75:1). All isolates of C. albicans were uniformly sensitive to all the azoles, but only 50% were sensitive to amphotericin B and none to nystatin and flucytosine. Conclusions: This observational study identifies ALL and chronic lymphocytic leukemia (CLL) as the forms of hematological malignancy predominantly associated with candidemia; specifies risk factors and chemotherapeutic agents predisposing patients towards its occurrence; reports a preponderance of C. tropicalis among the causative agents and finds voriconazole to be the most effective antifungal agent against the recovered isolates. This information could assist in tailoring prophylactic and therapeutic antifungal practices for this infection, according to local epidemiological and mycological characteristics. Keywords: Hematological malignancies, Candida infections, Antifungal resistance, Candida tropicalis, Non-Candida albican

Loop-Mediated Isothermal Amplification (Lamp) Assay: Principles and Applications

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Identification of extracellular matrix proteins of rice (Oryza sativa L.) involved in dehydration-responsive network: a proteomic approach

Water-deficit or dehydration impairs almost all physiological processes and greatly influences the geographical distribution of many crop species. It has been postulated that higher plants rely mostly on induction mechanisms to maintain cellular integrity during stress conditions. Plant cell wall or extracellular matrix (ECM) forms an important conduit for signal transduction between the apoplast and symplast and acts as front-line defense, thereby playing a key role in cell fate decision under various stress conditions. To better understand the molecular mechanism of dehydration response in plants, four-week-old rice seedlings were subjected to progressive dehydration by withdrawing water and the changes in the ECM proteome were examined using two-dimensional gel electrophoresis. Dehydration-responsive temporal changes revealed 192 proteins that change their intensities by more than 2.5-fold, at one or more time points during dehydration. The proteomic analysis led to the identification of about 100 differentially regulated proteins presumably involved in a variety of functions, including carbohydrate metabolism, cell defense and rescue, cell wall modification, cell signaling and molecular chaperones, among others. The differential rice proteome was compared with the dehydration-responsive proteome data of chickpea and maize. The results revealed an evolutionary divergence in the dehydration response as well as organ specificity, with few conserved proteins. The differential expression of the candidate proteins, in conjunction with previously reported results, may provide new insight into the underlying mechanisms of the dehydration response in plants. This may also facilitate the targeted alteration of metabolic routes in the cell wall for agricultural and industrial exploitation

Attractive Sugar Bait Formulation for Development of Attractive Toxic Sugar Bait for Control of Aedes aegypti (Linnaeus)

Background. Attractive toxic sugar bait (ATSB), based on “attract and kill” approach, is a novel and promising strategy for mosquito control. Formulation of an attractive sugar bait (ASB) solution by selecting an efficient olfaction stimulant and preparation of an optimized sugar-attractant dosage is a significant component for the success of the approach. Methods. Current study evaluated relative potential of nine ASBs, formulated by combination of sugar and fresh fruit juices (guava, mango, muskmelon, orange, papaya, pineapple, plum, sweet lemon, and watermelon) in attracting Aedes aegypti adults. Freshly extracted and 48-hour-fermented juices were combined with 10% sucrose solution (w/v) in 1 : 1 ratio. Cage bioassays were conducted against two laboratory strains (susceptible: AND-Aedes aegypti; deltamethrin-selected: AND-Aedes aegypti-DL10) and two field-collected strains (Shahdara strain of Aedes aegypti: SHD-Delhi; Govindpuri strain of Aedes aegypti: GVD-Delhi). Each of the nine ASBs was assayed, individually or in groups of three, for its attraction potential based on the relative number of mosquito landings. The data were analysed for statistical significance using PASW (SPSS) software 19.0 program. Results. The prescreening bioassay with individual ASB revealed significantly higher efficacy of ASB containing guava/plum/mango juice than that containing six other juices (p<0.05) against both the laboratory and field strains. The bioassay with three ASBs kept in one cage, one of the effective ASBs and two others randomly selected ASBs, also showed good attractancy of the guava/plum/mango juice-ASB (p<0.05). The postscreening assays with these three ASBs revealed maximum attractant potential of guava juice-sucrose combination for all the four strains of Ae. aegypti. Conclusion. Guava juice-ASB showed the highest attractancy against both laboratory and field-collected strains of Ae. aegypti and can be used to formulate ATSB by combining with a toxicant. The field studies with these formulations will ascertain their efficacy and possible use in mosquito management programs