The popular lecture for the undergraduate students of agriculture to know about the application of biotechnology in agriculture science graduates. Some of the major break through inventions how it impact on agriculture research and development
Genomics and its application in crop improvementKhemlata20
meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Genomics and its application in crop improvementKhemlata20
meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Gene prediction is the process of determining where a coding gene might be in a genomic sequence. Functional proteins must begin with a Start codon (where DNA transcription begins), and end with a Stop codon (where transcription ends).
A physical map of a chromosome or a genome that shows the physical locations of genes and other DNA sequences of interest. Physical maps are used to help scientists identify and isolate genes by positional cloning.
According to the ICSM (Intergovernmental Committee on Surveying and Mapping), there are five different types of maps: General Reference, Topographical, Thematic, Navigation Charts and Cadastral Maps and Plans.
Morphological, Cytological and Biochemical MarkersJay Khaniya
I've put a lot of effort for create this presentation. This'll help to lot of biotechnology and agricultural students for there assignments and exam study.
Presenter: Dr. Marie Haga
Executive Director, Global Crop Diversity Trust.
Facing demographic and climate changes, our best and most important tool to develop a resilient agricultural system is found in the natural diversity of crops and within crops. The Global Crop Diversity Trust (Crop Trust) works to safeguard the most important collections of crop diversity in genebanks around the world. This global common good will guarantee farmers and plant breeders have access to the raw materials needed to improve our crops, and ultimately, feed the world.
Gene prediction is the process of determining where a coding gene might be in a genomic sequence. Functional proteins must begin with a Start codon (where DNA transcription begins), and end with a Stop codon (where transcription ends).
A physical map of a chromosome or a genome that shows the physical locations of genes and other DNA sequences of interest. Physical maps are used to help scientists identify and isolate genes by positional cloning.
According to the ICSM (Intergovernmental Committee on Surveying and Mapping), there are five different types of maps: General Reference, Topographical, Thematic, Navigation Charts and Cadastral Maps and Plans.
Morphological, Cytological and Biochemical MarkersJay Khaniya
I've put a lot of effort for create this presentation. This'll help to lot of biotechnology and agricultural students for there assignments and exam study.
Presenter: Dr. Marie Haga
Executive Director, Global Crop Diversity Trust.
Facing demographic and climate changes, our best and most important tool to develop a resilient agricultural system is found in the natural diversity of crops and within crops. The Global Crop Diversity Trust (Crop Trust) works to safeguard the most important collections of crop diversity in genebanks around the world. This global common good will guarantee farmers and plant breeders have access to the raw materials needed to improve our crops, and ultimately, feed the world.
Bacillus thuringiensis, an aerobic, Gram positive, spore forming bacterium produces unique proteinaceous crystalline parasporal inclusions during sporulation which have insecticidal properties. Besides being widely used as an insecticide in agriculture, Bt has been found to be useful in several fields like medicine, endoparasite control, bacteriocin production as well as enzyme production. Parasporin, a new category of bacterial parasporal protein capable of discriminately killing the cancer cells have been discovered. There are six classes of parasporins having different mode of action and cell specificities against cancer and tumor cells (Ohba et al., 2009).Bt proteins have also been used successfully to suppress the population levels of medically important Dipteran pests like mosquitoes by use of mosquitocidal strains that produce Cry proteins (Zhang et al., 2012) as well as potential therapeutic agent against protozoan disease Leishmaniases (El-Sadawy et al., 2008). Crystal proteins, like Cry5B from Bacillus thuringiensis are found to be safe to vertebrates and have been shown to have efficacy against intestinal hookworm parasites (Capello et al., 2006). Thus the multifarious applications of Bacillus thuringiensis have made it a microbe to reckon with and further study its genome for future developments.
The Moss- Physcomitrella patens : A Novel Model System for Plant Development...Senthil Natesan
The moss P.patens has been used as a versatile experimental model organism for the past 80 years and it falls in the division Bryophyta. Being relatively simple in morphology and it generates only few tissues that contain limited number of cell fates (Mark leech et al., 1993), it is extensively being undertaken by plant biologists on both basic and applied strategies covering major areas namely developmental biology, evolution, systems biology, biotechnology ,biodiversity etc., As the organism is predominantly haploid in nature, it is evident that it could allow to develop insights on straight forward investigation/understanding of plant systems and hence, it is amenable for genetic and molecular level studies (Cove., 2009). The availability of complete genome sequence information, genetic and physical map ease the utilization of P.patens in all most all the fields of biology (Yasuko Kamisugi., 2008). It is the only land plant with an efficient system of homologous recombination in its nuclear DNA by which specific gene targeting could be achieved and the strategy of loss of function mutants can be generated by RNAi approach. In this context, the functional genomics of P.patens helps in identifying novel genes which could be employed in metabolic engineering and stress tolerance like drought, salt and osmotic stress thus helps in improving the crop plant performance. Moreover, it serves as a valuable platform for the production of recombinant pharmaceuticals (Anna K. Beike., 2010) Thus, the transfer of novel genes from P.patens has a greater biotechnological impact and may help in better public acceptance. Hence, this presentation aims to confine the advantages of this model plant in plant molecular research by discussing its efficiency in reproduction, range of technologies applied, some interesting characteristic features behind this model and chosen case studies will establish the model behaving as a well-versed medium for wide variety of approaches
TNAU Seed portal- Tamil Nadu Agricultural University Seed portalSenthil Natesan
Seed play an important role in any technology embedding and we have to produce pure, quality, resistant, healthy seeds for production of healthy food to satisfy our needs.The vast variety of information regarding seeds is scattered and no such organized one stop database available at present
Hence information regarding quality seed production, maintenance of seed quality and purity, minimum seed standards of the crop, Varietal characters, DUS characters and many are incorporated in the user friendly interface TNAU SEED PORTAL .
Majority of agronomic traits are quantitative and are controlled polygenetically.Instead of producing transgenic plants through single gene transfer many researchers are attempting on multigene engineering. The simultaneous transfer of multiple genes in to plants will enable us to produce plants with more desirable characters. Engineering of genes coding for complete metabolic pathways, bacterial operons or biopharmaceuticals that require an assembly of complex multisubunit proteins etc are some of the successful examples of multigene engineering.
In recent years, antibodies have become increasingly accepted as therapeutics for human diseases, particularly for cancer, viral infection and autoimmune disorders.
Monoclonal antibodies (Mabs) have been used as diagnostic and analytical reagents since hybridoma technology was invented in 1975.
“man-made antibodies.” was named by Cesar Milstein, who was one of the inventors of monoclonal antibody technology.
Until the late 1980’s, antibody technology relied primarily on animal immunization and the expression of engineered antibodies.
New insights into the human genome by ENCODE project Senthil Natesan
It’s been ten years since scientists sequenced the human genome. But what do all these letters?
Researchers could identify in its 3 billion letters many of the regions that code for proteins, but those make
up little more than 1% of the genome, contained in around 21,000 genes a few familiar objects in an otherwise stark and unrecognizable landscape. Many biologists suspected that the information responsible
for the wondrous complexity of humans lay somewhere in the ‘deserts’ between the genes (The ENCODE Project Consortium, 2012).
Interpreting the human genome sequence is one of the leading challenges of 21st century biology
(Collins et al., 2003). In 2003, the National Human Genome Research Institute (NHGRI) embarked on an
ambitious project the Encyclopedia of DNA Elements (ENCODE), aiming to delineate all of the functional elements encoded in the human genome sequence (The ENCODE Project Consortium 2004). To further
this goal, NHGRI organized the ENCODE Consortium, an international group of investigators with diverse
backgrounds and expertise in production and analysis of high-throughput functional genomic data. In a pilot project phase spanning 2003–2007, the Consortium applied and compared a variety of experimental and computational methods to annotate functional elements in a defined 1% of the human genome (The ENCODE Project Consortium, 2007)
Nanobiotechnological applications in dna therapySenthil Natesan
Gene therapy is a form of molecular medicine that has the potential to influence significantly human health in this 21st century. It promises to provide new treatments for a large number of inherited and acquired diseases (Verma and Weitzman, 2005). The basic concept of gene therapy is simple which includes introduction of a piece of genetic material into target cells that will result in either a cure for the disease or a slowdown in the progression of the disease. To achieve this goal, gene therapy requires technologies capable of gene transfer into a wide variety of cells, tissues, and organs. A key factor in the success of gene therapy is the development of delivery systems that are capable of efficient gene transfer in a variety of tissues, without causing any associated pathogenic effects. Vectors based upon many different viral systems, including retroviruses, lentiviruses, adenoviruses, and adeno-associated viruses, currently offer the best choice for efficient gene delivery.
How to deal with complex virus disease problems Senthil Natesan
Group of emerging plant viruses causing economically significant damage to a broad range of field crops, vegetables, ornamentals, fruits, etc.
Viruses can not move by themselves
and they need a “safe” vehicle to spread from plant to plant one such is thrips -Naidu A. Rayapati, Presentation at CPMB, TNAU 19th,August 2009
this will be useful to understand about the new topics such as abzymes, ribozymes and also isoenzymes. You have to clear that ribozymes are not protein. because all enzymes are proteins but all proteins are not enzymes except ribozymes
Genomic aided selection for crop improvementtanvic2
In last Several years novel genetic and genomics approaches are expended. Genetics and genomics have greatly enhanced our understanding of the structural and functional aspects of plant genomes.
Mining Phenotypes: How to set up a reverse genetics experiment with an Arabid...adcobb
In this lesson, students will mine data from Araport.org to design and propose a reverse genetics experiment using a known Arabidopsis mutant. They will select a treatment to reveal phenotypic dfifferences between wild type and mutant Arabidopsis. Student handout and teacher resources are available at www.Araport.org, teacher resources. Suitable for grades 9-12 or first year undergraduate students.
Molecular markers (DNA markers) have entered the scene of genetic improvement in a wide range of horticultural crops. Among the major traits targeted for improvement in horticultural breeding programmes are disease and pest resistance, fruit yield and quality, tree shape, floral morphology, drought tolerance and dormancy. The development of molecular techniques for genetic analysis has led to a great increase in the knowledge of horticultural genetics and understanding and behavior of their genomes. These molecular techniques in particular, molecular markers, have been used to monitor DNA sequence variation in and among the species and create new sources of genetic variation by introducing new and favorable traits from landraces, wild relatives and related species and to fasten the time taken in conventional breeding. Today, markers are also being used for, genetic mapping, gene tagging and gene introgression from exotic and wild species.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
Genome project of Human and methods of sequencing human genome; Genome project of Rice and its post genome sequencing era; Arabidopsis genome project: Why Rice and Arabidopsis chosen for genome project?
Centre of innovation, Agricultural College and Research Institute,MaduraiSenthil Natesan
Establishment Central Instrumentation facility with the cost of 6.03 crore to take up multidisciplinary research project at AC&RI,Madurai. The analytical platform includes UP-HPLC for amino acid analysis, XRF for micronutrient analysis and GC-MS for metabolic profiling. The imaging facilities like upright, inverted and Florence microscope established for imaging pathogen & Insects. The molecular biology lab with real time PCR will help for the gene expression studies.
The agriculture sector employs nearly half of the workforce in the country. However, it contributes to 17.5% of the GDP (at current prices in 2015-16).Agriculture sector’s contribution has decreased from more than 50% of GDP in the 1950s to 15.4% in 2015-16 (at constant prices). This slides discuss about Indian agriculture status and problems and solutions.
paper presented during the National seminar on Challanges and Innovative approaches in Crop Improvement at AC&RI, Madurai. during December 16-17, 2014 .Germplasm conservation in Oil Palm by Dr P. Murugesan Indian Institute of Oil Palm Research
Improvement of Medicinal Plants: Challenges and Innovative ApproachesSenthil Natesan
Paper Presented during the National seminar on Challenges and Innovative approaches in crop improvement held at AC&RI, Madurai , TNAU by
Dr.P. Manivel, Directorate of Medicinal and Aromatic Plants Research, Boriavi-387310, Anand, Gujarat
Castor is an oilseed plant which is earning attention on researchers in recent days. Because of this, the gemplasms of ancient varieties were now recovered and grown in trial fields for getting genetically superior variety.
As a result, in Castor and Tapioca research station there a variety named YRCH (Yethapur Ricinus Communis Hybrid) with all desired traits which are essential for a plant both phenotypically and genetically was developed.
Triacylglycerols produced by plants are one of the most energy-rich and abundant forms of reduced carbon available from nature. Given their chemical similarities, plant oils represent a logical substitute for conventional diesel, a non-renewable energy source. However, as plant oils are too viscous for use in modern diesel engines, they are converted to fatty acid esters. Apart from seed oil vegetative tissue is potential source as bio mass for biofuel production, taking 15 tonnes per hectare as an average dry matter yield for a perennial grass, an oil content of 20– 25% by weight will produce about 3400 l of biodiesel (Heaton et al., 2004). There is growing interest in engineering green biomass to expand the production of plant oils as feed and biofuels. Here, we show that PHOSPHOLIPID: DIACYLGLYCEROL ACYLTRANSFERASE1 (PDAT1) is a critical enzyme involved in triacylglycerol (TAG) synthesis in leaves. Overexpression of PDAT1 increases leaf TAG accumulation, leading to oil droplet overexpansion through fusion. Ectopic expression of oleosin promotes the clustering of small oil droplets. Coexpression of PDAT1 with oleosin boosts leaf TAG content by up to 6.4% of the dry weight without affecting membrane lipid composition and plant growth. PDAT1 overexpression stimulates fatty acid synthesis (FAS) and increases fatty acid flux toward the prokaryotic glycerolipid pathway (Julian at al..2013). First, an Arabidopsis thaliana gene diacylglycerol acyltransferase (DGAT) coding for a key enzyme in triacylglycerol (TAG) biosynthesis, was expressed in tobacco under the control of a strong ribulose-biphosphate carboxylase small subunit promoter. This modification led to up to a 20-fold increase in TAG accumulation in tobacco leaves and translated into an overall of about a twofold increase in extracted fatty acids (FA) up to 5.8% of dry biomass in Nicotiana tabacum cv Wisconsin, and up to 6% in high-sugar tobacco variety NC-55 ( Andrianovet al 2010). Therefore Biotechnology has important and perhaps critical part to play in large-scale development of Biodiesel.
Vaccines have been revolutionary for the prevention of infectious diseases. Despite worldwide immunization of children against the six devastating diseases, 20% of infants are still left un-immunized; responsible for approximately two million unnecessary deaths every year, especially in the remote and impoverished parts of the globe. This is because of the constraints on vaccine production, distribution and delivery. One hundred percent coverage is desirable, because un-immunized populations in remote areas can spread infections and epidemics in the immunized safe areas, which have comparatively low herd immunity. For some infectious diseases, immunizations either do not exist or they are unreliable or very expensive. Immunization through DNA vaccines is an alternative but is an expensive approach, with disappointing immune response. Hence the search is on for cost-effective, easy-to-administer, easy-to-store, fail-safe and socio-culturally readily acceptable vaccines and their delivery systems. As Hippocrates said, Let thy food be thy medicine, scientists suggest that plants and plant viruses can be genetically engineered to produce vaccines against diseases such as dental caries; and life-threatening infections like diarrhea, AIDS, etc (Lal et al., 2007)
Cellular signal transduction pathways under abiotic stressSenthil Natesan
Abiotic stresses, especially cold, salinity and drought, are the primary causes of crop loss worldwide. Plant adaptation to environmental stresses is dependent upon the activation of cascades of molecular networks involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Plants have stress-specific adaptive responses as well as responses which protect the plants from more than one environmental stress. There are multiple stress perception and signaling pathways, some of which are specific, but others may cross-talk at various steps (Knight & knight ,2001).Many cold induced pathways are activated to protect plants from deleterious effects of cold stress, but till date, most studied pathway is ICE-CBF-COR signaling pathway (Miura and Furumoto,2013 ) . The Salt-Overly-Sensitive (SOS) pathway, identified through isolation and study of the sos1, sos2, and sos3 mutants, is essential for maintaining favorable ion ratios in the cytoplasm and for tolerance of salt stress (shi .et al ,2002). Both ABA-dependent and -independent signaling pathways appear to be involved in osmotic stress tolerance (Nakashima and shinozaki, 2013) .ROS play a dual role in the response of plants to abiotic stresses functioning as toxic by-products of stress metabolism, as well as important signal transduction molecules and the ROS signaling networks can control growth, development, and stress response ( Mahajan,s and Tuteja, 2005) .
TNAU CRMD - A Customer Relationship Management datahouse for TNAUSenthil Natesan
Every great business starts with a great relationship. Every great relationship starts with You.
The strategy for establishing, developing and maintaining these relationships is CRM. (Customer Relationship Management).
The system that support this strategy is TNAU CRMD software.
TNAU CRMD offers unrivalled flexibility to design CRM applications and processes based on our needs.
TNAU PDB- Tamil Nadu Agricultural University Proteome Database-Black gram pro...Senthil Natesan
In India, blackgram is the main edible crop ranking fourth among the pulses. There is a need to increase the performance of pulse crops, particularly in developing countries, where most grain legume production is for human consumption and demand is increasing due to population increase.Investigation was carried out on the possible effects of artificial ageing on dry seeds of blackgram. We have analyzed the quantitative and qualitative proteome changes in artificially aged dry seeds compared with that in control and the results were presented herein.Fresh seeds taken as control and 6 days artificially seeds as test.There were totally 59 spots detected both in fresh and accelerated aged seeds. Among these 16 spots differentially were expressed by artificial ageing, including 4 up regulated spots and 12 down regulated ones.
The reference 2D-PAGE gel shows the position of each identified protein in control. The entire list of protein can also be obtained by selecting the crop variety displayed inside the table. By selecting the spot in the gel image the entire information about that protein in both control as well as test can be obtained.All the reference maps are also displayed under 2D gel section for a quick reference.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...
Genomics platform for agriculture-CAT lecture
1. Prof. Senthil Natesan
Department of Biotechnology, AC&RI, Madurai
Bio-Technology……
Genomics platform for agriculture
www.tnau.ac.in Department of
Biotechnology,
Tamil Nadu Agricultural University AC&RI,
2. “….. the best teaching can be done only when there is a direct …..
situation in which the student discusses the ideas,
thinks about the things, and talks about the things.
It’s impossible to learn very much by simply sitting in a lecture,
or even by simply doing problems that are assigned ……”
Richard Feynman 1963
4. Crop and plant genomes and their application. The figure gives the approximate timeline of when crop genomes were sequenced along with the
underlying techniques and sequencing strategy used. Hybrid strategies which use BAC by BAC and WGS are indicated by the placement of
a genome twice. Also note that the distinction between pure NGS and Hybrid sequencing is sometimes arbitrary as many genome projects rely on
previously generated Sanger sequences. In addition, some major applications are marked by symbols: Grains for an improvement in grain quality, a
flower for flowering time and a tomato for a tomato ripening trai
Department of Biotechnology, AC&RI, Madurai-www.tnaugenomics.com
5. Examples of the range of phenotypic variation in maize germplasm held
in the CIMMYT genebank (Photo provided by Dr. Taba Suketoshi)
Department of Biotechnology, AC&RI ,Madurai-www.tnaugenomics.com
7. Humans Have Limited Molecular
Diversity
0.09%
Zhao et al, 2000, PNAS
1.34%
Department of Biotechnology, AC&RI, Madurai-www.tnaugenomics.com
8. Maize diversity is greater than the difference
between human and chimps
Tenallion et al, 2001, PNAS
1.42%
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
9. Arabidopsis Sequencing Facts
• Arabidopsis has a small (125 Mb) sized-genome on 5
chromosomes
-Human has 3,000 Mb on 23 chromosomes
-Maize has 2,500 Mb on 10 chromosomes
-Medicago has 520 Mb on 8 chromosomes
-Rice has 430 Mb on 12 chromosomes
-Lily has 50,000 Mb on 12 chromosomes
• Arabidopsis has approx. 25,500 genes
-
humans have slightly fewer, about
24,000
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
10. The Human Genome Project
The most public large-scale sequencing project has been the Human Genome
Project. Started by the Department of Energy, who realized the possible
implications on human health-related issues, it began in 1990, with
collaborative funding from a number of sources.
After much drama and bickering in the scientific community, the genome was
actually sequenced twice by 2 different groups (the publicly funded group
headed by Francis Collins and Craig Venter’s company Celera) and the
completion announced simultaneously at a joint press conference*.
*Published separately: International Human Genome Sequencing Consortium
(2001) and Venter et al. (2001)
J. Craig Venter (l) and Francis Collins (r)
at the historic announcement June 26,
2000
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
11. Whole genome sequencing
While we will not go into technical details or pros and cons here, you should be
aware of the two main approaches to sequencing a whole genome.
“Top-down” strategy:
An anchored physical map
is needed; overlapping
clones (a “minimal tiling
path”) are sequenced in
order. Since the positions
of the clones (and therefore
the sequences) are already
known, little post-
sequencing work is
needed.
Images from The Creative Science Quarterly, Helmut Kae (2003)
http://www.scq.ubc.ca/?p=392
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
12. Automated sequencing reactions - each reaction can resolve 600 to 750 bp
(labeled with fluorescent dyes)
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
13. FISH analysis of the centromeric
core of chromosome 5 in Rice
The schema of constructing a physical map
ofrice chromosome 5.
14. Comparing genomes: Example from the grasses
This is now one of the most well-known figures in plant
comparative genomics.
This consensus comparative map of 7 grasses
shows how the genomes can be aligned in
terms of “rice linkage blocks” (Gale and Devos
1998). Any radial line starting at rice, the
smallest genome and innermost circle, will pass
through regions of similar gene content in each
of the other species.
Therefore a gene on the chromosome of one
grass species can be anticipated to be present
in a predicted location on a specific
chromosome of a number of other grass family
species. This has facilitated much sharing
among researchers working on any of these
species and others that may be also related
(Phillips & Freeling 1998).
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
15. SNP discovery- Early methods
• Re-sequencing of PCR amplicons with or without pre-screening
• Direct sequencing of DNA segments amplified by PCR)from several individuals is the most direct way to identify SNP
polymorphisms
• Alternatively, an allele-specific-PCR or primer-extension assay may be developed relatively straightforwardly.
Rafalski 2002 Curr Opin Plant Biol 5 :94-100
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
16. DNA sequencing output
If you have DNA sequence produced from a PCR product or a library of
ESTs, the sequence of your DNA segment(s) will be given to or, more usually,
emailed or electronically transferred to you..
If the data is in the chromatogram form, you will need to manually generate
a text file such as the one below (by “reading” the bases yourself) or, more
typically, use one of the many software programs available to do this for you.
If you retrieve a sequence from a public database, it will already be in this
format for you.
The first 480 bases of the DNA sequence of GAN, a drought tolerance
related gene in Arabidopsis (GenBank Accession AY986818).
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
17. What are markers?
Markers, in the context of breeding, are identifiers of characteristics of
the phenotype and/or genotype of an individual; their inheritance can be
followed through generations.
Markers can be:
Morphological: variation in traits which is scorable in single plants (eg
flowering time)
Biochemical: reflect variation at the protein or metabolite level (eg
isozymes)
Molecular: reflect variation at the DNA sequence level (eg
microsatellites)
In these beans, color could be a morphological marker,
as could size, plant height, etc. The gel picture on the
previous slide showed a molecular marker that
identified differences between the various plant lines.
Image: CGIAR
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
18. Protein markers & quality of wheat
12
7
8
12 10
5
9
HMW glutenin
-gliadins
albumins
globulins
LMW glutenins (B
subunits)
, ,-gliadins
LMW glutenins (C
subunits)
albumins
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
19. Repetitive sequence
primer I
primer II
plant A
plant B
microsatellite
plant A
plant B
flanking region II
flanking region I
specific primers were designed corresponding to
flanking sequence of microsatellite
PCR analysis and analyze on 6 %denaturing
polyacrylamide gel with silver staining
A BSchematic of SSR
assay
Department of Biotechnology,AC&RI, Madurai- www.tnaugenomics.com
20. Detection of PCR product
www.tnau.ac.in Department of
Biotechnology,
Tamil Nadu Agricultural University AC&RI,
22. Microsatellite markers polymorphism between
parental lines and rice hybrids
Tamilkumar et al.,2009
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
24. Testing genetic purity of hybrid seeds of CORH3 using the SSR
marker RM 234
Lane 2 = TNAUCMS2A (CMS line), Lane 3 = CB87R (restorer line). DNA was
isolated from single seedlings of the CORH3 hybrid, PCR analysis was performed and
genotype assessed (Lanes 4–12) Off type in Lanes 8.
Tamilkumar et al.,2009
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
25. Advantages of MAB: Cost
Depending on the trait and the cost of phenotyping, MAB may also cut
down on costs. The costs of field plots, greenhouse space, labour, and
the measuring of some traits can be expensive, or in the case of certain
diseases, impossible.
Of course, some phenotyping will always be required to confirm results,
but MAB can decrease the amount of phenotyping in many situations.
The ability to test for the presence of
a certain allele rather than waiting
until the associated trait can be seen
can decrease the amount of
phenotyping that is necessary.
Products such as the FTA cards
shown at left can make DNA
extractions, and therefore marker
work, easier.
Image: TM Fulton
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
26. Advantages of MAB: knowledge
Using markers can also give us a deeper understanding of the traits we are
selecting for and HOW they work. This could allow for more efficient selection in
the future.
For example, once a marker – trait
correlation is established, the marker can
be used to clone the gene, and more
thoroughly study its action. In tomato, a
major QTL affecting fruit weight was
cloned and found to control carpel cell
number early in fruit development (Frary
et al. 2000).
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
27. MAB: Costs
Using molecular markers requires the use of specific laboratory
equipment, at the very least a PCR (polymerase chain reaction)
thermalcycler and electrophoresis and visualization equipment. So
start-up costs can be high (although these may be compensated for by
later savings).
A PCR machine and a basic agarose electrophoresis apparatus.
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
28. Crop Domestication:
From plants in the wild to our kitchen
Over time, humans have selected those plants that exhibited traits that
are in OUR (humans) interests: larger fruit, more kernels.
Examples of cultivated varieties and their wild relatives.
Images: Steven Tanksley, John Doebley
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
29. Crop Domestication
Crop domestication inherently decreases genetic variation, by the
selection of just a few of the available lines (those with traits seen as
desirable by the selectors, ie. humans)
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
30. Traits selected for by humans
Traits that have been selected for by humans include:
• Determinate growth habit (flowering occurs at the top of the plant,
preventing further growth)
• Retention of mature seed on the plant (loss of grain shattering)
• Synchronous ripening, shorter maturity
• Lower content of bitter tasting and harmful compounds
• Reduced sprouting, higher seed dormancy
• improved harvest index (the proportion of the plant which is used); larger
seed or fruit size
• elimination of seeds, such as in banana
Many of these trait changes reduce the ability for the plant to compete
in the wild, and also decrease the genetic variability remaining in the
crop.
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
31. Consequences of loss of genetic diversity:
One result of less diversity is that consumers and farmers are now
accustomed to, and demand, uniformity: round red apples, plants all the
same height in the field.
But the loss of genetic diversity can have devastating consequences, such
as the Irish potato blight of 1850, the Southern corn leaf blight of 1970, and
the current crisis in banana, Black Sigatoka disease, shown above.
Banana image Copyright 2001 by The American Phytopathological Society, http://www.apsnet.org/education/feature/banana/; apple photo
ourtesy of New York Apple Association
32. Genetic diversity is available in
genebanks
Fortunately, many wild relatives of our crops have have been saved in
genebanks around the world.
Alleles that can be naturally introgressed in from wild relatives of crop plants
can not only increase their genetic diversity but improve them for traits that
would not be predicted by looking at their phenotypes (Tanksley and
McCouch 1997).
As of 2006, the CGIAR centers
(Consultative Group on
International Agricultural
Research) together contain
more than 650,000 accessions
of crop, forage and agroforestry
species (2006 Bioversity
International).
Photo: CGIAR-IRRI
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
33. Germplasm banks
Most crops have many accessions stored in genebanks, or germplasm
banks, that are available free of charge or with a shipping and handling
fee, for example, the
USDA-ARS National Plant Germplasm System (http://www.ars-
grin.gov/npgs/).
The CGIAR system has a number of genebanks around the world:
http://www.cgiar.org/impact/accessions.htm.
The International Rice Research
Institute (IRRI) genebank in Los
Banos, Philippines, has over
80,000 accessions of rice.
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
34. Science 20 :November 2009:
The B73 Maize Genome:
Complexity, Diversity, and Dynamics
Nature 457, 551-556 (29 January 2009)
The Sorghum bicolor genome
Nature Biotechnology 30, 549–554 (13 May 2012)
Genome sequence of foxtail millet
Staking of key traits through marker
assisted breeding
Department of Biotechnology,AC&RI,Madurai- www.tnaugenomics.com
35. UMI 79 UMI 936(W)X
F1
F2
F6
Molecular tagging of downy mildew resistance in maize and introgression into elite inbred
lines
phi053(21.3)
bnlg420(0)
dup23(80.4)
bnlg1185(141.7)
umc1223(53.8)
umc1594(0)
bnlg420(61.2)
bnlg197(111.4)
phi053(45.7)
umc1594(828.9)
phi088(596.49)
phi046(605.44)
bnlg197(511.5)
bnlg420(318.4)
phi073(344)
bnlg1035(313.4)
phi053(297.9)
umc1223(234.4)
phi029(168.08)
phi099(159.0)
phi104127(38.0)
IBM2 2008 neighbors2
24 recombinant
Nair et al.,2005 Kashmiri ,2010
Figure 12 a. Genetic linkage map showing location of SDM QTL on chromosome 3 on different mapping population
CM139 XNAI116 UMI 79XUMI936(w)
- SDM QTL
Screening of RILs in artificial
epiphytotic condition for
sorghum downy mildew (P.
sorghi) reaction
Recom
binant
lines
X Elite
inbred
Hybrid
F1
36. Marker assisted introgression of LycE /CrtRB1 gene
for enhanced Pro VitA in maize
The back cross progenies of UMI 1200 ( 1.16
μg/g β-carotene and popular inbred) x
HP467-15 (5.10 μg/g β-carotene and CIMMYT
donor) are under evaluation.
HPLC analysis also revealed a considerable
improvement in the β-carotene of selected F1
(1.50 μg/g ) and BC1F1 progenies ( 2.2 μg/g) as
compared to the well-adapted low β-carotene
inbred (UMI 1200).
BC2 F2 progenies
UMI 1200
HP467-15
Particula
rs
UMI
1200
HP 467-
15
Standard β-
carotene -Type I
β-
carotene
(μg/g)
1.16 5.1 10.0
Peak area 85,95
9
1,58,628 3,83,815
Rt 23.50 23.50 23.50
37. CrtRB1 gene based marker screening
HPLC Screening- UMI 1200
β-carotene 1.16 µg/g
UMI 1200 : Allele 2
HP467-15 : Allele 1
UMI 176 : Yellow grain
β-carotene : 7.92 µg/g
crtRB1 3’TE gene Specific marker
296+875 bp
296+1221 bp
543 bp
HP 467-15 Yellow grain
β-carotene : 5.10 µg/g
Co-dominant PCR assays for analyzing allelic variations at 3’TE site of crtRB1 gene among the
maize inbreds. : Lane 1-UMI 936(O); Lane2-UMI 112; Lane 3- UMI 101; Lane 4-UMI 80; Lane 5-UMI 61;
Lane6-UMI 176; Lane 7-UMI 1230; Lane 8-UMI 551; Lane 9- HP467-15; Lane 10-UMI 190; Lane 11-UMI
285; Lane 12-UMI 1200; Lane 13-UMI 69; Lane 14- UMI 395, Lane M: 100 bp DNA ladder.
Thirusenthura selvi et al. 2014 Food Biotechnology 28:41-49