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

Primary meningeal sarcoma (fibrosarcoma) of cervical spine in an 11 yr old boy: An extremely rare case report

Primary meningeal sarcoma is a rare tumor in pediatric age group. Here we were reporting an extremly rare case report of an 11 year old boy presented with quadriparesis and bladder involvement. MRI revealed a cervical dural based tumor with extension to cord parenchyma and neural foramina involving paravertebral tissue. The histopathology revealed mesenchymal tumor with malignant potential which on immunohistochemical (IHC) study found to be vimentin positive fibrosarcoma

Facebook Prophet Library prediction-based Energy Harvested MAC Protocol (FPEH-MAC)

Data transfer within severe time constraints is crucial for wireless sensor networks used in mission-critical applications, such as industrial control and disaster monitoring. In such applications, exceeding time constraints and facing limitations in longevity can pose threats to human life. The primary option for powering wireless sensor networks is to utilize ambient energy sources like solar energy, thermal energy, etc., which are abundant in nature The lifetime and latency of these networks depend on a well-implemented duty cycle-based MAC protocol, and maximizing the duty cycle is achieved through efficient utilization of harvested and residual energy. Since harvested energy is inherently unpredictable, appropriate forecasting techniques are required. In this study, a prediction-based Energy Harvested MAC protocol (FPEH-MAC) based on the Facebook Prophet library is proposed to maximize the predicted duty cycle of the MAC protocol by forecasting harvested and residual energy. Additionally, this MAC protocol demonstrates an increase in residual energy and duty cycle, ensuring an extended lifecycle for the wireless sensor network. The suggested protocol was evaluated for latency, throughput, percentage increase in residual energy, and packet delivery ratio using OMNET, INET, Python, and MATLAB. The results of the analysis indicate that the proposed technique increases residual energy by 1.2%, enhances throughput by 33.33%, and reduces latency by 9.6% when compared to previous work

Microleakage of bonded amalgam restorations using different adhesive agents with dye under vacuum: An in vitro study

Aim: In an effort to minimize tooth preparation, yet provide additional retention to compromised tooth structure, bonded amalgam restorations were introduced. Various resin-based adhesives have been tried earlier under bonded amalgam restorations. Still there are controversies regarding the outcome of bonded amalgam restorations regarding their adaptability to the tooth structure and microleakage. Therefore, this study was undertaken to compare the microleakage of bonded amalgam restorations using different adhesive materials. Materials and Methods: Standard Class I cavities were prepared on occlusal surfaces of 60 human molars. Teeth (n=60) were divided into three groups according to the material employed, as follows: group I: amalgam with glass ionomer cement (GIC) (type I); group II: amalgam with resin cement (Panavia F 2.0) and group III: amalgam with Copalex varnish as a control. Following restoration, the teeth were submitted to thermal cycling. The teeth were subsequently immersed in 2% rhodamine B dye under vacuum for 48 hours and sectioned to allow the assessment of microleakage under stereomicroscope. Results: The values were tabulated and the results were statistically analyzed using analysis of variance (ANOVA), Tukey′s post hoc test and Kruskal-Wallis test. Amalgam with type I GIC showed the least leakage with no statistically significant difference (P value 0.226) when compared to amalgam with Panavia F 2.0 and amalgam with varnish (P value 0.107). Conclusion: It can be concluded that bonded amalgam with type I GIC is a good alternative to amalgam with resin cement (Panavia F 2.0) and amalgam with varnish for large restorations, with the added advantages of GICs. Clinical Significance: Bonded amalgam restorations prevent over-preparation and reduce the tooth flexure. GIC type I under amalgam provides chemical bonding in between amalgam and tooth structure and thus reduces the microleakage

Burden of hepatitis C virus infection and its genotypes among the blood donors at Tirupati, Andhra Pradesh

Background: Safe blood donation remains a challenge in resource limited countries. False positive serological tests lead to wastage of large number of blood units. Nucleic acid amplification test (NAAT) technology has greatly enhanced the accuracy in identification of transfusions transmitted infections. Methods: The present study was undertaken to study the seroprevalence of hepatitis C virus (HCV) and asses the concordance between seropositivity with the presence of HCV ribonucleic acid (RNA) and to know the distribution pattern of HCV genotypes in healthy blood donors. Results: Among the 9287 donors screened (88.3% males), 7153 (77%) were voluntary donors while 2134 (23%) were replacement donors. Among blood donors, 27 (0.3%) samples tested HCV seropositive. Among 27 anti-HCV positive samples only 11 (41%) were found positive for HCV RNA. Among the 5 samples subjected to sequencing, three were found to be genotype 1a while two were genotype 3a. Conclusions: Our observations suggest that implementing NAAT test for HCV screening will be helpful in minimizing false-positive test results in the Indian setting

Additional file 1: of Genome-wide identification of novel intergenic enhancer-like elements: implications in the regulation of transcription in Plasmodium falciparum

Supplementary Figures (S1-S9). (DOCX 2070 kb

Additional file 2: Table S4. of Genome-wide identification of novel intergenic enhancer-like elements: implications in the regulation of transcription in Plasmodium falciparum

List of the enhancer-like elements identified in Plasmodium falciparum. (XLS 71 kb