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RNA not only serves as a central intermediate between genome and proteome but also plays an important regulatory role in cellular biology. Major advancements in high-throughput sequencing have allowed the generation of large quantities of genomic and RNA data over a short time span. The potency of RNA sequencing (RNA-seq) has facilitated the identification of transcripts, the quantification of gene expression, and the detection of the RNA function. This technology has been supplemented by the codevelopment of bioinformatics algorithms for sifting through and analyzing the data. RNA-seq datasets have been generated to decipher, characterize, and quantify various sets of RNA molecules produced in cells. This can reveal critical information on the genes that are turned on, their expression level, and the regulatory triggers. This is particularly useful in the discovery and mapping of the noncoding RNA species that regulate a variety of biological functions. In this chapter, we discuss about the various next-generation sequencing platforms and applications of RNA-seq.

Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (SNAT) and acetyl-serotonin methyltransferase (ASMT) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of OsTDC5 and OsASMT18, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.

Glycine max is a worldwide leading economic crop and its seeds are deepening with proteins and oils which supply food and sustenance to all being. Various amounts of alimentary constituents are racked up in the G. max seed in the period of its ontogenesis. Thus, grasping the regulation of biological functions during seed enlargement belong to the basics for crop enhancement. The gene regulatory characteristics of miRNAs in G. max attracted us to focus on its target gene prediction, gene ontology (GO) analysis and expression pattern to their miRNA target genes, which suggest significant involvement in the development of G. max seed. Seven miRNAs have been found from the differential gene expression analysis of development stage 0–4 mm vs. 12–16 mm of G. max seed on the statistical parameter of p value ≤ 0.05 by computational-based microarray data analysis for miRNA target gene prediction. The miRNA target prediction analysis showed total 23 genes that were cleaved from 6 miRNAs, and computationally validated by identifying t-plots of miRNA targets using CleaveLand tool. GO results confirmed that the differentially expressed target genes could be classified into 20 molecular function categories, 73 biological process categories, and 10 cell components categories. On the basis of GO results, two genes were found to be significantly involved in the developmental process of G.max seed. The first miRNA target gene Glyma.01g119500 was predicted to annotate for embryo development ending in seed dormancy, seed dormancy, seed maturation, and seed germination. The second miRNA target gene Glyma.15g005300 was found to be involved in the regulation of seed germination. The Soybean eFP browser analysis suggests that the gene Glyma.01g119500 and Glyma.15g005300 reaches its maximum expression level of 35.88 and 26.6 respectively in the Soybean data source. The present study provides an avenue to explore more genomic and proteomic information about G. max seed developmental stage-specific miRNA target genes.

A plant&rsquo, s response to stress conditions is governed by intricately coordinated gene expression. The microRNAs (miRs) have emerged as relatively new players in the genetic network, regulating gene expression at the transcriptional and post-transcriptional level. In this study, we performed comprehensive profiling of miRs in roots of the naturally salt-tolerant Pokkali rice variety to understand their role in regulating plant physiology in the presence of salt. For comparisons, root miR profiles of the salt-sensitive rice variety Pusa Basmati were generated. It was seen that the expression levels of 65 miRs were similar for roots of Pokkali grown in the absence of salt (PKNR) and Pusa Basmati grown in the presence of salt (PBSR). The salt-induced dis-regulations in expression profiles of miRs showed controlled changes in the roots of Pokkali (PKSR) as compared to larger variations seen in the roots of Pusa Basmati. Target analysis of salt-deregulated miRs identified key transcription factors, ion-transporters, and signaling molecules that act to maintain cellular Ca2+ homeostasis and limit ROS production. These miR:mRNA nodes were mapped to the Quantitative trait loci (QTLs) to identify the correlated root traits for understanding their significance in plant physiology. The results obtained indicate that the adaptability of Pokkali to excess salt may be due to the genetic regulation of different cellular components by a variety of miRs.

Increasing incidence of viral infections in crop plants adversely affects their growth and yield. Tomato (Solanum lycopersicum) is considered to be a favorite host for viruses with over 50 species of begomoviruses naturally infecting this crop. Tomato leaf curl virus (ToLCV) is among the most widespread and devastating begomoviruses affecting tomato production. microRNAs (miRs) have been established as key regulators of gene expression and plant development. The miR pathways are disturbed during infection by viruses. Thus, comprehension of regulatory miR networks is crucial in understanding the effect of viral pathogenicity. To identify key miRs involved in ToLCV infection, a high throughput approach involving next generation sequencing was employed. Healthy and infected leaf tissues of two tomato varieties, differing in their susceptibility to ToLCV infection were analyzed. NGS data analysis followed by computational predictions, led to identification of 91 known miRs, 15 novel homologs and 53 novel miRs covering two different varieties of tomato, susceptible (Pusa Ruby) and tolerant (LA1777) to ToLCV infection. The cleaved targets of these miRs were identified using online available degradome libraries from leaf, flower and fruit of tomato and showed their involvement in various biological pathways through KEGG Orthology. With detailed comparative profiling of expression pattern of these miRs, we could associate the specific miRs with the resistant and infected genotypes. This study depicted that in depth analysis of miR expression patterns and their functions will help in identification of molecules that can be used for manipulation of gene expression to increase crop production and developing resistance against diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12298-017-0482-3) contains supplementary material, which is available to authorized users.

Light and temperature are two major environmental factors influencing plant growth and development. High temperature caused by increasing global warming and greenhouse gases has become a worldwide concern. In plants, it triggers various morphological, biochemical and physiological changes that adversely influence growth and development leading to substantial decrease in crop yield. The declining food production and the requirements of the rapidly growing population pose further threat to global food security. Plants have elaborate genetic and epigenetic regulatory mechanisms to endure through the unfavorable abiotic conditions. The induction of heat stress response at the genetic level involves de-regulation of transcription factors and chaperones which play an indispensable role in acclimation to heat. The epigenetic regulation includes induction or repression of specific microRNAs (miRs) that target a variety of transcripts. This is a signature response by plants that is observed in almost all stresses such as high light intensities, drought and salinity. Since earlier reports have indicated a strong relationship between light and temperature signaling pathways in plants, so their integration in influencing the miR based regulatory networks needs to be elucidated. Here we present the mirador (window designed to command an extensive outlook) on the potential role of miRs in regulating plant growth and development in synergistic response to light and heat networks.

This work is about designing of thermal aware low power Vedic multiplier using Stub-Series Terminated Logic (SSTL). The design of Vedic multiplier is a part of Vedic arithmetic circuits design project. “Urdhva-Tiryagbhyam” sutra is used to design the Vedic multiplier. SSTL135_R is minimum I/O power consumer. SSTL135_DCI is maximum power consumer. When we use SSTL135_R in place of SSTL12, SSTL12_DCI, SSTL15, and SSTL135_DCI, there is 42.5%, 82.7%, 28.12%, and 72.9% reduction in I/O power at 21 0 C, 40 0 C, 53.5 0 C and 56.7 0 C. This design is implemented on Artix-7 FPGA using Verilog as hardware description language and Xilinx ISE 14.1 as simulator.

In this paper, we have designed an energy efficient Vedic Divider using an ancient Vedic mathematics technique known as "Paravart- yaYojayet". ParavartyaYojayet is a Sanskrit name which means transpose and adjust. Vedic mathematical formulas are used to solve tedious and cum- bersome arithmetic operations. Today's world demands implementation of techniques which take lesser time and are energy efficient so we have de- signed a Vedic divider to solve long divisions in seconds. Our design con- sists of 2 inputs for dividend and divisor and 2 outputs that are remainder and quotient. Many researchers have done research work on Vedic mathe- matics to solve DSP operations using Urdhava-Triyagbhayam multiplica- tion sutra, to design asynchronous Vedic DSP processor core and lots more. In our paper we have implemented our code on Xilinx ISE Design Suite 14.2 and results were tested on 28nm FPGA platform. We have done power analysis by varying frequencies and capacitance to make our Vedic divider energy efficient. Analysis results that the maximum power is consumed at 2.2GHz and minimum power is consumed at 1.2GHz. In respect of capac- itance maximum power is consumed at 100pF and minimum power is con- sumed at 20pF.

Stub-Series Terminated Logic (SSTL) IO standards and theory of Vedic Mathematics are used in design of Vedic multiplier. This vedic multiplier is a part of Vedic arithmetic circuits design project for Vedic Processor Design. This Vedic multiplier design is based on the formula “Urdhva-Tiryagbhyam” means Vertical and cross wise. SSTL135_R is minimum I/O power consumer. SSTL135_DCI is maximum power consumer. There is 8.27% reduction in Total power when we use SSTL12_DCI in place of SSTL135_DCI at 56.7C. There is 14.19% reduction in IO power when we use SSTL12_DCI in place of SSTL135_DCI at 56.7C. There is 50% reduction in Total power when we use SSTL135_R in place of SSTL135_DCI at 56.7C. There is 85.16% reduction in IO power when we use SSTL135_R in place of SSTL135_DCI at 56.7C. This design is implemented on 28nm FPGA using Verilog and Xilinx Integrated System Environment 14.1. There is no change in Leakage power with change in IO standards. Leakage power depends on ambient temperature. In the other words, leakage power is directly proportional to ambient temperature. Keywords–SSTL, Low Power, Vedic Multiplier, IO Standard, FPGA

High temperature and salinity stress are major factors limiting the growth and productivity of rice crop on a global scale. It is therefore an essential prerequisite to understand the molecular genetic regulation of plant responses to dual stresses. MicroRNAs (miRs) are recognized as key controllers of gene expression which act mainly at the post-transcriptional level to regulate various aspects of plant development. The present study attempts to investigate the miR circuits that are modulated in response to high temperature and salinity stress in rice. To gain insights into the pathway, preliminary miR profiles were generated using the next-generation sequencing (NGS) datasets. The identified molecules were filtered on the basis of fold differential regulation under high temperature, and time kinetics of their expression under the two individual stresses was followed to capture the regulatory windows. The analysis revealed the involvement of common miR regulatory nodes in response to two different abiotic stresses, thereby broadening our perspective about the stress-mediated regulatory mechanisms operative in rice.

ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.

Epigenetics is an upcoming field that studies the gene regulation of mitotically heritable genes which change the physiology of cells without altering the DNA sequence. Various epigenetic elements such as modification of histone proteins, methylation of DNA, chromatin modeling, and RNA-mediating silencing influence the regulation of genes at many levels, which leads to diseases such as cancer. All of these factors modulate gene expression in a tissue-specific manner. Bioinformatics is a successful approach in the field of molecular biology for studying epigenomics data. To generate these epigenomic data which can be analyzed using various bioinformatics tools and software, a variety of technologies are being used by researchers. Many biological databases which store a huge amount of information related to the modifications due to epigenetics are available online. With the help of these data, we can identify key target genes that can be manipulated to achieve some resistance against diseases caused by epigenetic factors.

Genome-wide, a gene can be designated as indispensable for the survival of a cell or an organism, and its interruption can lead to the malfunctioning or death of the organism. Due to its essentiality for survival, these could be proposed as novel and promising candidates for broad-spectrum drug targets, if these are conserved across a genus. Identification of essential gene has been done in many organisms, and interestingly, most of them were pathogenic in nature. The genome-scale elucidation of essential genes plays an important role in development and complete genome availability. At large scale, gene-inactivation technologies such as targeted gene inactivation, genetic footprinting, and transposon-based mutagenesis are controlled by essential genes. In silico, numerous strategies and tools also have been developed, such as subtractive genomics, essentiality base mapping, and target identification using phylogenetic profiling. Bioinformatic approaches can also be used to analyze experimentally generated data. This chapter is referred to provide an overview of some of these methodologies which are often used to identify essential genes and their functions and discuss advantage and drawbacks of the methods.

This paper deals with low power multiplier design that plays a significant role in green wireless communications systems. Over the period of time, researchers have proposed various multiplier designs in order to get high speed. Vedic multiplier is considered as one of the low power multiplier along with high speed as compared with traditional array and booth multipliers. Vedic Multiplier contains a total of sixteen algorithms/sutras for predominantly logical operations. This research focuses on thermal aspects and energy efficiency of wireless communications systems with the thermal aware low power design of Vedic Multiplier. Temperature plays an important role on the performance of any device. The primary purpose of this research is to enhance the thermal stability of the wireless communications. Energy efficient IO standards are used to decrease the power dissipation of Vedic Multiplier and that eventually decrease power dissipation of wireless communications systems. In order to study the effect of different process technology (40, 65, 90 nm) on our design, a novel design is implemented on 40, 65 and 90 nm based FPGA. In this work, we are integrating thermal aware design approach for energy efficient Vedic Multiplier on various FPGA using LVCMOS and HSTL I/O standard. LVCMOS is an acronym for Low Voltage Complementary Metal Oxide Semiconductor and HSTL is an acronym for High Speed Transceiver Logic. In this Vedic Multiplier, we are using three LVCMOS I/O standard and nine HSTL I/O standard. In order to test the thermal sustainability of our Vedic Multiplier design, we are testing it in three different room temperatures i.e. 20, 30, and 40 °C. Using LVCMOS25, there is 12.99, 19.23 and 10.28% reduction in power dissipation on 90, 65 and 40 nm FPGAs respectively. For LVCMOS25, when our Vedic Multiplier design is migrated from 40 nm design to 90 nm FPGA design, there is 87.72% reduction in power dissipation of Vedic Multiplier when temperature is kept constant at 20 °C. When temperature is scaled down from 50 to 20 °C there is 12.45, 14.93, 12.84, 9.45 and 8.48% saving in power dissipation on using HSTL_I, HSTL_I_12, HSTL_I_18, HSTL_I_DCI and HSTL_I_DCI_18 IO Standard respectively on 90 nm FPGA.

Increase in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by multiple genes coding for signaling molecules, ion transporters, metabolic enzymes and transcription regulators. MicroRNAs are key modulators of gene-expression that act at the post-transcriptional level by translation repression or transcript cleavage. They also play an important role in regulating plant’s response to salt-stress. In this work we adopted the approach of comparative and integrated data-mining to understand the miRNA-mediated regulation of salt-stress in rice. We profiled and compared the miRNA regulations using natural varieties and transgenic lines with contrasting behaviors in response to salt-stress. The information obtained from sRNAseq, RNAseq and degradome datasets was integrated to identify the salt-deregulated miRNAs, their targets and the associated metabolic pathways. The analysis revealed the modulation of many biological pathways, which are involved in salt-tolerance and play an important role in plant phenotype and physiology. The end modifications of the miRNAs were also studied in our analysis and isomiRs having a dynamic role in salt-tolerance mechanism were identified.

Multiplier is used for multiplication of a signal and a constant in Digital Signal Processing (DSP). 28nm tech-nology based Vedic multiplier is implemented with use of VHDL HDL, Xilinx ISE, Kintex-7 FPGA and Xpower Analyser. Vedic multiplier gains speed improvements by parallelizing the generation of partial prod-ucts with their concurrent summations. In this work, we are exploring the feasibility of Vedic multiplier in Data Encryption Algorithm, DSP, reliable system, multimedia and fault tolerant systems. In our work, we are using 11 different IO standards from HSTL (High Speed Transistor Logic) and LVCMOS (Low Voltage Comple-mentary Metal Oxide Semiconductor) family. IO standards are used to match the impedance of transmission line, input/output port and device. The energy-efficient multipliers play a significant role in portable computing and communication systems also. Here we are using Field Programmable Gate Array (FPGA) in order to re-duce the development cost. The development cost for Application Specific Integrated Circuits (ASICs) are high in compare to FPGA. Selection of the most energy efficient IO standards in place of signal gating is the main design methodology for design of energy efficient Vedic multiplier. There is 68.51%, 69.86%, 74.65%, and 78.39% contraction in total power of Vedic multiplier on 28nm Kintex-7 FPGA, when we use HSTL_II in place of HSTL_II_DCI_18 at 56.7oC, 53.5oC, 40oC and 21oC respectively.

microRNAs (miRs) are a class of 21-24 nucleotide long non-coding RNAs responsible for regulating the expression of associated genes mainly by cleavage or translational inhibition of the target transcripts. With this characteristic of silencing, miRs act as an important component in regulation of plant responses in various stress conditions. In recent years, with drastic change in environmental and soil conditions different type of stresses have emerged as a major challenge for plants growth and productivity. The identification and profiling of miRs has itself been a challenge for research workers given their small size and large number of many probable sequences in the genome. Application of computational approaches has expedited the process of identification of miRs and their expression profiling in different conditions. The development of High-Throughput Sequencing (HTS) techniques has facilitated to gain access to the global profiles of the miRs for understanding their mode of action in plants. Introduction of various bioinformatics databases and tools have revolutionized the study of miRs and other small RNAs. This review focuses the role of bioinformatics approaches in the identification and study of the regulatory roles of plant miRs in the adaptive response to stresses.

In this project, we are using LVCMOS and HSTL IO standards in order to match the resistance of input and output line, input and output port and Vedic multiplier. The primary purpose of Impedance matching is to eliminate transmission line reflection. Now, impedance matching is used to increase the stability of device with the help of IO standard. Therefore, selection of energy efficient IO standard will increase the energy efficiency of design under consideration. LVCMOS (Low Voltage Complementary Metal Oxide Semiconductor) and HSTL (High Speed Transceiver Logic) are energy efficient IO standard. Energy efficient IO standards are used to decrease the power dissipation of Vedic multiplier. Then, we try to achieve more energy efficiency with different technology (40nm, 65nm, 90nm) based FPGA. There is 95.07%, and 63.7% leakage power reduction with HSTLII_D18 IO standard, when we migrate our design from Virtex-5 to Virtex-6, and Virtex-4 respectively. With the energy efficient LVCMOS18 IO standard, there is 94.64% 61.57% reduction in leakage power, when we migrate our design from Virtex-5 to Virtex-6 and Virtex-4.

In this work, we are integrating thermal aware design approach in energy efficient Vedic multiplier on FPGA. In the beginning of this universe, Veda describes heat receiving from the Sun god as Suryamrit (Surya i.e. Sun +Amrit i.e. Nectar= Suryamrit i.e. Nectar coming from the Sun God). Now, whole world is feeling anxious about temperature. How our thinking pattern is changing with evolution of mankind? This paper deals with that question and the whole work is going in direction to get solution of this problem with mechanism of ambient (room) temperature scaling and energy efficient LVCMOS I/O standard. LVCMOS is an acronym for low voltage complementary metal oxide semiconductor. In this Vedic multiplier, we are using three LVCMOS I/O standard. LVCMOS12 is available only in 65nm and 40nm FPGA. Rest LVCMOS18 and LVCMOS25 is available among 40nm, 65nm and 90nm FPGA. In order to test the thermal sustainability of our Vedic multiplier, we are testing it in three different room temperature 20°C, 30°C, and 40°C. Using LVCMOS25, there is 12.99%, 19.23% and 10.28% reduction in power dissipation on 90nm, 65nm and 40nm respectively. For LVCMOS25, when our Vedic multiplier design is migrated from 40nm design to 90nm design, there is 87.72% reduction in power dissipation of Vedic multiplier when temperature is constant 20°C.

Low Voltage Digitally Controlled Impedance (LVDCI) is an I/O standard available on FPGA. This design is LVDCI IO standard based Energy Efficient Vedic Multiplier Design on FPGA. Selection of IO standard play an important role in power dissipation of design. Therefore, we are going to select the most energy efficient IO standards in LVDCI family for Vedic Multiplier. This Vedic multiplier design is a part of project of Vedic arithmetic circuits. The final deliverable of this project is Vedic Processor by merging both concepts of Veda, first book of this world, and the latest technology of this world. In order to test thermal aware design, we want to see that how does an electronic device behave if we change the temperature of surrounding in which it is working. For that purpose we have taken temperatures of four different regions. Furnace Creek Ranch is area of North America recorded the highest temperature of the world that is 56.7°C [1]. Approximately, 53.5°C is the maximum temperature recorded in Mohenjo-Daro situated in Sindh Pakistan [1]. We have also taken median temperature of Delhi i.e. 40°C and standard normal temperature i.e. 21°C. We are operating Vedic Multiplier with the four different temperature and different LVDCI IO standard and observe device performance, and power dissipation. When we use 28nm FPGA under room temperature of 40°C, there are 93.42%, 92.6%, 93.99%, 93.59% and 89.79% reduction in total power dissipation of Vedic multiplier using LVDCI 15, LVDCI 18, LVDCI DV2 15, LVDCI DV2 18 and HSLVDCI 15 respectively. Similarly, when we use 28nm FPGA, there is approximately 90-96% reduction in leakage power dissipation of Vedic multiplier using different LVDCI and different temperature. There is no change in I/O power with change in temperature for uniform IO standard. When we use different IO standard of LVDCI family, there is significant reduction in leakage power. FPGA based on 28 nm technology is more energy efficient than 40 nm technology based FPGA.

Introduction Spontaneous recurrent pneumothorax during pregnancy is a rare condition. Few cases have been reported previously in the literature. There is no universal guideline for the management of this condition. Treatment options include conservative management with intercostal drain and surgical management in the form of thoracotomy or video-assisted thoracoscopy. Case presentation We report a case of recurrent spontaneous pneumothorax in a 38-year-old Afro-Caribbean woman on her third trimester of pregnancy. The disease was managed with the insertion of an intercostal drain on three occasions, which was then followed by surgical intervention immediately after pregnancy. Conclusion The diagnosis of pneumothorax should be considered in the differential diagnosis of pregnant women experiencing chest pain and dyspnoea. No adverse maternal or foetal outcome has been reported in well-managed cases. Management involves good coordination between the obstetric and surgical teams.

A 29-year-old woman with known ulcerative colitis developed a right-sided abdominal pain a day after preterm vaginal delivery at 30 weeks. She did not have any nausea, vomiting and had normal bowel movements. The observations were within normal limits and white cell counts were marginally elevated with a normal C reactive protein. A large ovarian vein thrombosis on the left side was an incidental finding on a CT of the abdomen and pelvis undertaken to establish the cause for abdominal pain. The patient was managed by a multidisciplinary team and was treated with anticoagulants for 6 months. This case illustrates that the incidence of pelvic venous thrombosis may be higher in pregnancy and puerperium.