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Increased stable integration efficiency in CHO cells through enhanced nuclear localization of Bxb1 serine integrase

Mammalian display is an appealing technology for therapeutic antibody development. Despite the advantages of mammalian display, such as full-length IgG display with mammalian glycosylation and its inherent abi...

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Screening of Candida spp. in wastewater in Brazil during COVID-19 pandemic: workflow for monitoring fungal pathogens

Fungal diseases are often linked to poverty, which is associated with poor hygiene and sanitation conditions that have been severely worsened by the COVID-19 pandemic. Moreover, COVID-19 patients are treated w...

Transgenic Arabidopsis thaliana plants expressing bacterial γ-hexachlorocyclohexane dehydrochlorinase LinA

γ-Hexachlorocyclohexane (γ-HCH), an organochlorine insecticide of anthropogenic origin, is a persistent organic pollutant (POP) that causes environmental pollution concerns worldwide. Although many γ-HCH-degra...

Molecular and agro-morphological characterization of new barley genotypes in arid environments

Genetic diversity, population structure, agro-morphological traits, and molecular characteristics, are crucial for either preserving genetic resources or developing new cultivars. Due to climate change, water ...

Microvesicles-delivering Smad7 have advantages over microvesicles in suppressing fibroblast differentiation in a model of Peyronie’s disease

This study compared the differences of microvesicles (MVs) and microvesicles-delivering Smad7 (Smad7-MVs) on macrophage M1 polarization and fibroblast differentiation in a model of Peyronie’s disease (PD).

Improvement and prediction of the extraction parameters of lupeol and stigmasterol metabolites of Melia azedarach with response surface methodology

Melia azedarach is known as a medicinal plant that has wide biological activities such as analgesic, antibacterial, and antifungal effects and is used to treat a wide range of diseases such as diarrhea, malaria, ...

Dual release of daptomycin and BMP-2 from a composite of β-TCP ceramic and ADA gelatin

Antibiotic-containing carrier systems are one option that offers the advantage of releasing active ingredients over a longer period of time. In vitro sustained drug release from a carrier system consisting of ...

Minimizing IP issues associated with gene constructs encoding the Bt toxin - a case study

As part of a publicly funded initiative to develop genetically engineered Brassicas (cabbage, cauliflower, and canola) expressing Bacillus thuringiensis Crystal ( Cry )-encoded insecticidal (Bt) toxin for Indian an...

Activating the healing process: three-dimensional culture of stem cells in Matrigel for tissue repair

To establish a strategy for stem cell-related tissue regeneration therapy, human gingival mesenchymal stem cells (hGMSCs) were loaded with three-dimensional (3D) bioengineered Matrigel matrix scaffolds in high...

Co-overexpression of chitinase and β-1,3-glucanase significantly enhanced the resistance of Iranian wheat cultivars to Fusarium

Fusarium head blight (FHB) is a devastating fungal disease affecting different cereals, particularly wheat, and poses a serious threat to global wheat production. Chitinases and β-glucanases are two important ...

A new mRNA structure prediction based approach to identifying improved signal peptides for bone morphogenetic protein 2

Signal peptide (SP) engineering has proven able to improve production of many proteins yet is a laborious process that still relies on trial and error. mRNA structure around the translational start site is imp...

Correction: Transcriptomic and targeted metabolomic analyses provide insights into the flavonoids biosynthesis in the flowers of Lonicera macranthoides

The original article was published in BMC Biotechnology 2024 24 :19

A model approach to show that monocytes can enter microporous β-TCP ceramics

β-TCP ceramics are versatile bone substitute materials and show many interactions with cells of the monocyte-macrophage-lineage. The possibility of monocytes entering microporous β-TCP ceramics has however not...

Nutritional composition, lipid profile and stability, antioxidant activities and sensory evaluation of pasta enriched by linseed flour and linseed oil

Pasta assortments fortified with high quality foods are a modern nutritional trends. This study, explored the effects of fortification with linseed flour (LF) and linseed oil (LO) on durum wheat pasta characte...

In vitro assessment of the effect of magnetic fields on efficacy of biosynthesized selenium nanoparticles by Alborzia kermanshahica

Cyanobacteria represent a rich resource of a wide array of unique bioactive compounds that are proving to be potent sources of anticancer drugs. Selenium nanoparticles (SeNPs) have shown an increasing potentia...

ECM-mimetic, NSAIDs loaded thermo-responsive, immunomodulatory hydrogel for rheumatoid arthritis treatment

Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease, and it leads to irreversible inflammation in intra-articular joints. Current treatment approaches for RA include non-steroidal anti-infla...

Development of a chemiluminescence assay for tissue plasminogen activator inhibitor complex and its applicability to gastric cancer

Venous thromboembolism (VTE), is a noteworthy complication in individuals with gastric cancer, but the current diagnosis and treatment methods lack accuracy. In this study, we developed a t-PAIC chemiluminesce...

High-performance internal circulation anaerobic granular sludge reactor for cattle slaughterhouse wastewater treatment and simultaneous biogas production

This research investigates the efficacy of a high-performance pilot-scale Internal Circulation Anaerobic Reactor inoculated with Granular Sludge (ICAGSR) for treating cattle slaughterhouse wastewater while con...

Hindering the biofilm of microbial pathogens and cancer cell lines development using silver nanoparticles synthesized by epidermal mucus proteins from Clarias gariepinus

Scientists know very little about the mechanisms underlying fish skin mucus, despite the fact that it is a component of the immune system. Fish skin mucus is an important component of defence against invasive ...

3D printing of Ceffe-infused scaffolds for tailored nipple-like cartilage development

The reconstruction of a stable, nipple-shaped cartilage graft that precisely matches the natural nipple in shape and size on the contralateral side is a clinical challenge. While 3D printing technology can eff...

A cleavable peptide adapter augments the activity of targeted toxins in combination with the glycosidic endosomal escape enhancer SO1861

Treatment with tumor-targeted toxins attempts to overcome the disadvantages of conventional cancer therapies by directing a drug’s cytotoxic effect specifically towards cancer cells. However, success with targ...

Multiprotein collagen/keratin hydrogel promoted myogenesis and angiogenesis of injured skeletal muscles in a mouse model

Volumetric loss is one of the challenging issues in muscle tissue structure that causes functio laesa . Tissue engineering of muscle tissue using suitable hydrogels is an alternative to restoring the physiological...

Analysis of the impact of pluronic acid on the thermal stability and infectivity of AAV6.2FF

The advancement of AAV vectors into clinical testing has accelerated rapidly over the past two decades. While many of the AAV vectors being utilized in clinical trials are derived from natural serotypes, engin...

Rice yellow mottle virus is a suitable amplicon vector for an efficient production of an anti-leishmianiasis vaccine in Nicotiana benthamiana leaves

Since the 2000’s, plants have been used as bioreactors for the transient production of molecules of interest such as vaccines. To improve protein yield, “amplicon” vectors based on plant viruses are used. Thes...

Extraction and analysis of high-quality chloroplast DNA with reduced nuclear DNA for medicinal plants

Obtaining high-quality chloroplast genome sequences requires chloroplast DNA (cpDNA) samples that meet the sequencing requirements. The quality of extracted cpDNA directly impacts the efficiency and accuracy o...

Transcriptomic and targeted metabolomic analyses provide insights into the flavonoids biosynthesis in the flowers of Lonicera macranthoides

Flavonoids are one of the bioactive ingredients of Lonicera macranthoides ( L. macranthoides ), however, their biosynthesis in the flower is still unclear. In this study, combined transcriptomic and targeted metabo...

The Correction to this article has been published in BMC Biotechnology 2024 24 :33

Effects of solid lipid nanocarrier containing methyl urolithin A by coating folate-bound chitosan and evaluation of its anti-cancer activity

Nanotechnology-based drug delivery systems have received much attention over the past decade. In the present study, we synthesized Methyl Urolithin A-loaded solid lipid nanoparticles decorated with the folic a...

Neq2X7: a multi-purpose and open-source fusion DNA polymerase for advanced DNA engineering and diagnostics PCR

Thermostable DNA polymerases, such as Taq isolated from the thermophilic bacterium Thermus aquaticus , enable one-pot exponential DNA amplification known as polymerase chain reaction (PCR). However, properties oth...

A solution for highly efficient electroporation of primary cytotoxic T lymphocytes

Cytotoxic T lymphocytes (CTLs) are central players in the adaptive immune response. Their functional characterization and clinical research depend on efficient and reliable transfection. Although various metho...

Adsorption of Hg 2+ /Cr 6+ by metal-binding proteins heterologously expressed in Escherichia coli

Removal of heavy metals from water and soil is a pressing challenge in environmental engineering, and biosorption by microorganisms is considered as one of the most cost-effective methods. In this study, the m...

Derivation of a novel antimicrobial peptide from the Red Sea Brine Pools modified to enhance its anticancer activity against U2OS cells

Cancer associated drug resistance is a major cause for cancer aggravation, particularly as conventional therapies have presented limited efficiency, low specificity, resulting in long term deleterious side eff...

Polyphyllin B inhibited STAT3/NCOA4 pathway and restored gut microbiota to ameliorate lung tissue injury in cigarette smoke-induced mice

Smoking was a major risk factor for chronic obstructive pulmonary disease (COPD). This study plan to explore the mechanism of Polyphyllin B in lung injury induced by cigarette smoke (CSE) in COPD.

Quantifying carboxymethyl lysine and carboxyethyl lysine in human plasma: clinical insights into aging research using liquid chromatography-tandem mass spectrometry

The objective of this study was to establish a methodology for determining carboxymethyl lysine (CML) and carboxyethyl lysine (CEL) concentrations in human plasma using liquid chromatography-tandem mass spectr...

Iron/Copper/Phosphate nanocomposite as antimicrobial, antisnail, and wheat growth-promoting agent

One of the current challenges is to secure wheat crop production to meet the increasing global food demand and to face the increase in its purchasing power. Therefore, the current study aimed to exploit a new ...

Staphopain mediated virulence and antibiotic resistance alteration in co-infection of Staphylococcus aureus and Pseudomonas aeruginosa : an animal model

Polymicrobial communities lead to worsen the wound infections, due to mixed biofilms, increased antibiotic resistance, and altered virulence production. Promising approaches, including enzymes, may overcome th...

Strain-specific features of Pleurotus ostreatus growth in vitro and some of its biological activities

The production of Pleurotus ostreatus mycelium as a promising object for use in food and other industries is hampered by a lack of information about the strain-specificity of this fungus mycelium growth and its a...

Antibacterial, antibiofilm, and anticancer activity of silver-nanoparticles synthesized from the cell-filtrate of Streptomyces enissocaesilis

Silver nanoparticles (Ag-NPs) have a unique mode of action as antibacterial agents in addition to their anticancer and antioxidant properties. In this study, microbial nanotechnology is employed to synthesize ...

Deep orange gene editing triggers temperature-sensitive lethal phenotypes in Ceratitis capitata

The Mediterranean fruit fly, Ceratitis capitata , is a significant agricultural pest managed through area-wide integrated pest management (AW-IPM) including a sterile insect technique (SIT) component. Male-only re...

Characterization, modeling, and anticancer activity of L.arginase production from marine Bacillus licheniformis OF2

L-arginase, is a powerful anticancer that hydrolyzes L-arginine to L-ornithine and urea. This enzyme is widely distributed and expressed in organisms like plants, fungi, however very scarce from bacteria. Our ...

Green and environmentally friendly synthesis of silver nanoparticles with antibacterial properties from some medicinal plants

Recently there have been a variety of methods to synthesize silver nanoparticles, among which the biosynthesis method is more noticeable due to features like being eco-friendly, simple, and cost-efficient. The...

Reaping the benefits of liquid handlers for high-throughput gene expression profiling in a marine model invertebrate

Modern high-throughput technologies enable the processing of a large number of samples simultaneously, while also providing rapid and accurate procedures. In recent years, automated liquid handling workstation...

Induction of antimicrobial, antioxidant metabolites production by co-cultivation of two red-sea-sponge-associated Aspergillus sp. CO2 and Bacillus sp. COBZ21

The growing spread of infectious diseases has become a potential global health threat to human beings. According to WHO reports, in this study, we investigated the impact of co-cultivating the isolated endophy...

A novel starch-active lytic polysaccharide monooxygenase discovered with bioinformatics screening and its application in textile desizing

Lytic polysaccharide monooxygenases (LPMOs) catalyzing the oxidative cleavage of different types of polysaccharides have potential to be used in various industries. However, AA13 family LPMOs which specificall...

Tuning spacer length improves the functionality of the nanobody-based VEGFR2 CAR T cell

The chimeric antigen receptor-expressing T (CAR-T) cells for cancer immunotherapy have obtained considerable clinical importance. CAR T cells need an optimized intracellular signaling domain to get appropriate...

Fabrication and characterization of metformin-loaded PLGA/Collagen nanofibers for modulation of macrophage polarization for tissue engineering and regenerative medicine

In tissue engineering (TE) and regenerative medicine, the accessibility of engineered scaffolds that modulate inflammatory states is extremely necessary. The aim of the current work was to assess the efficacy ...

Production of a potential multistrain probiotic in co-culture conditions using agro-industrial by-products-based medium for fish nutrition

Probiotics are viable microorganisms that when administered in adequate amounts confer health benefits to the host. In fish, probiotic administration has improved growth, and immunological parameters. For this...

Research on the targeted improvement of the yield of a new VB 12 -producing strain, Ensifer adhaerens S305, based on genomic and transcriptomic analysis

Vitamin B 12 (VB 12 ) has a wide range of applications and high economic value. In this study, a new strain with high VB 12 production potential, Ensifer adhaerens S305, was identified in sewage. Because E. adhaerens

Validation and calibration of a novel GEM biosensor for specific detection of Cd 2+ , Zn 2+ , and Pb 2+

In this study, we designed a novel genetic circuit sensitive to Cd 2+ , Zn 2+ and Pb 2+ by mimicking the CadA/CadR operon system mediated heavy metal homeostasis mechanism of Pseudomonas aeruginosa . The regular DNA m...

Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach

Goat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis...

The transcriptional factor Clr-5 is involved in cellulose degradation through regulation of amino acid metabolism in Neurospora crassa

Filamentous fungi are efficient degraders of plant biomass and the primary producers of commercial cellulolytic enzymes. While the transcriptional regulation mechanisms of cellulases have been continuously exp...

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Current research in biotechnology: Exploring the biotech forefront

2019, Current Research in Biotechnology

Biotechnology is an evolving research field that covers a broad range of topics. Here we aimed to evaluate the latest research literature, to identify prominent research themes, major contributors in terms of institutions, countries/re-gions, and journals. The Web of Science Core Collection online database was searched to retrieve biotechnology articles published since 2017. In total, 12,351 publications were identified and analyzed. Over 8500 institutions contributed to these biotechnology publications, with the top 5 most productive ones scattered over France, China, the United States of America, Spain, and Brazil. Over 140 countries/regions contributed to the biotechnology research literature, led by the United States of America, China, Germany, Brazil, and India. Journal of Bioscience and Bioengineer-ing was the most productive journal in terms of number of publications. Metabolic engineering was among the most prevalent biotechnology study themes, and Escherichia coli and Saccharomyces cerevisiae were frequently used in biotechnology investigations, including the biosynthesis of useful biomolecules, such as myo-inositol (vitamin B8), mono-terpenes, adipic acid, astaxanthin, and ethanol. Nanoparticles and nanotechnology were identified too as emerging biotechnology research themes of great significance. Biotechnology continues to evolve and will remain a major driver of societal innovation and development.

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An Introduction to Biotechnology

Varsha gupta.

5 Institute of Biosciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, UP India

Manjistha Sengupta

6 George Washington University, Washington DC, USA

Jaya Prakash

7 Orthopaedics Unit, Community Health Centre, Kanpur, UP India

Baishnab Charan Tripathy

8 School of Life sciences, Jawaharlal Nehru University, New Delhi, India

Biotechnology is multidisciplinary field which has major impact on our lives. The technology is known since years which involves working with cells or cell-derived molecules for various applications. It has wide range of uses and is termed “technology of hope” which impact human health, well being of other life forms and our environment. It has revolutionized diagnostics and therapeutics; however, the major challenges to the human beings have been threats posed by deadly virus infections as avian flu, Chikungunya, Ebola, Influenza A, SARS, West Nile, and the latest Zika virus. Personalized medicine is increasingly recognized in healthcare system. In this chapter, the readers would understand the applications of biotechnology in human health care system. It has also impacted the environment which is loaded by toxic compounds due to human industrialization and urbanization. Bioremediation process utilizes use of natural or recombinant organisms for the cleanup of environmental toxic pollutants. The development of insect and pest resistant crops and herbicide tolerant crops has greatly reduced the environmental load of toxic insecticides and pesticides. The increase in crop productivity for solving world food and feed problem is addressed in agricultural biotechnology. The technological advancements have focused on development of alternate, renewable, and sustainable energy sources for production of biofuels. Marine biotechnology explores the products which can be obtained from aquatic organisms. As with every research area, the field of biotechnology is associated with many ethical issues and unseen fears. These are important in defining laws governing the feasibility and approval for the conduct of particular research.

Introduction

The term “ biotechnology” was coined by a Hungarian engineer Karl Ereky, in 1919, to refer to the science and methods that permit products to be produced from raw materials with the aid of living organisms. Biotechnology is a diverse field which involves either working with living cells or using molecules derived from them for applications oriented toward human welfare using varied types of tools and technologies. It is an amalgamation of biological science with engineering whereby living organisms or cells or parts are used for production of products and services. The main subfields of biotechnology are medical (red) biotechnology, agricultural (green) biotechnology, industrial (white) biotechnology, marine (blue) biotechnology, food biotechnology, and environmental biotechnology (Fig. 1.1 .). In this chapter the readers will understand the potential applications of biotechnology in several fields like production of medicines; diagnostics; therapeutics like monoclonal antibodies, stem cells, and gene therapy; agricultural biotechnology; pollution control ( bioremediation); industrial and marine biotechnology; and biomaterials, as well as the ethical and safety issues associated with some of the products.

Major applications of biotechnology in different areas and some of their important products

The biotechnology came into being centuries ago when plants and animals began to be selectively bred and microorganisms were used to make beer, wine, cheese, and bread. However, the field gradually evolved, and presently it is the use or manipulation of living organisms to produce beneficiary substances which may have medical, agricultural, and/or industrial utilization. Conventional biotechnology is referred to as the technique that makes use of living organism for specific purposes as bread/cheese making, whereas modern biotechnology deals with the technique that makes use of cellular molecules like DNA, monoclonal antibodies, biologics, etc. Before we go into technical advances of DNA and thus recombinant DNA technology, let us have the basic understanding about DNA and its function.

The foundation of biotechnology was laid down after the discovery of structure of DNA in the early 1950s. The hereditary material is deoxyribonucleic acid (DNA) which contains all the information that dictates each and every step of an individual’s life. The DNA consists of deoxyribose sugar, phosphate, and four nitrogenous bases (adenine, guanine, cytosine, and thymine). The base and sugar collectively form nucleoside, while base, sugar, and phosphate form nucleotide (Fig. 1.2 ). These are arranged in particular orientation on DNA called order or sequence and contain information to express them in the form of protein. DNA has double helical structure, with two strands being complimentary and antiparallel to each other, in which A on one strand base pairs with T and G base pairs with C with two and three bonds, respectively. DNA is the long but compact molecule which is nicely packaged in our nucleus. The DNA is capable of making more copies like itself with the information present in it, as order or sequence of bases. This is called DNA replication. When the cell divides into two, the DNA also replicates and divides equally into two. The process of DNA replication is shown in Fig. 1.3 , highlighting important steps.

The double helical structure of DNA where both strands are running in opposite direction. Elongation of the chain occurs due to formation of phosphodiester bond between phosphate at 5′ and hydroxyl group of sugar at 3′ of the adjacent sugar of the nucleotide in 5–3′ direction. The sugar is attached to the base. Bases are of four kinds: adenine ( A ), guanine ( G ) (purines), thymine ( T ), and cytosine ( C ) (pyrimidines). Adenine base pairs with two hydrogen bonds with thymine on the opposite antiparallel strand and guanine base pairs with three hydrogen bonds with cytosine present on the opposite antiparallel strand

The process of DNA replication. The DNA is densely packed and packaged in the chromosomes. The process requires the action of several factors and enzymes. DNA helicase unwinds the double helix. Topoisomerase relaxes DNA from its super coiled nature. Single-strand binding proteins bind to single-stranded open DNA and prevent its reannealing and maintains strand separation. DNA polymerase is an enzyme which builds a new complimentary DNA strand and has proofreading activity. DNA clamp is a protein which prevents dissociation of DNA polymerase. Primase provides a short RNA sequence for DNA polymerase to begin synthesis. DNA ligase reanneals and joins the Okazaki fragments of the lagging strand. DNA duplication follows semiconservative replication, where each strand serves as template which leads to the production of two complimentary strands. In the newly formed DNA, one strand is old and the other one is new (semiconservative replication). DNA polymerase can extend existing short DNA or RNA strand which is paired to template strand and is called primer. Primer is required as DNA polymerase cannot start the synthesis directly. DNA polymerase is capable of proofreading, that is, correction of wrongly incorporated nucleotide. One strand is replicated continuously with single primer, and it is called as leading strand. Other strand is discontinuous and requires the addition of several primers. The extension is done in the form of short fragments called as Okazaki fragments. The gaps are sealed by DNA ligase. Replication always occurs in 5′–3′ direction

DNA contains whole information for the working of the cell. The part of the DNA which has information to dictate the biosynthesis of a polypeptide is called a “gene.” The arrangement or order of nucleotides determines the kind of proteins which we produce. Each gene is responsible for coding a functional polypeptide. The genes have the information to make a complimentary copy of mRNA. The information of DNA which makes RNA in turn helps cells to incorporate amino acids according to arrangement of letters for making many kinds of proteins. These letters are transcribed into mRNA in the form of triplet codon, where each codon specifies one particular amino acid. The polypeptide is thus made by adding respective amino acids according to the instructions present on RNA. Therefore, the arrangement of four bases (adenine, guanine, cytosine, and thymine) dictates the information to add any of the 20 amino acids to make all the proteins in all the living organisms. Few genes need to be expressed continuously, as their products are required by the cell, and these are known as “constitutive genes.” They are responsible for basic housekeeping functions of the cells. However, depending upon the physiological demand and cell’s requirement at a particular time, some genes are active and some are inactive, that is, they do not code for any protein. The information contained in the DNA is used to make mRNA in the process of “ transcription” (factors shown in Table 1.1 ). The information of mRNA is used in the process of “ translation” for production of protein. Transcription occurs in the nucleus and translation in the cytoplasm of the cell. In translation several initiation factors help in the assembly of mRNA with 40S ribosome and prevent binding of both ribosomal subunits; they also associate with cap and poly(A) tail. Several elongation factors play an important role in chain elongation. Though each cell of the body has the same genetic makeup, but each is specialized to perform unique functions, the activation and expression of genes is different in each cell. Thus, one type of cells can express some of its genes at one time and may not express the same genes some other time. This is called “temporal regulation” of the gene. In the body different cells express different genes and thus different proteins. For example, liver cell and lymphocyte, would express different genes. This is known as spatial regulation of the gene. Therefore, in the cells of the body, the activation of genes is under spatial regulation (cells present at different locations and different organs produce different proteins) and temporal regulation (same cells produce different proteins at different times). The proteins are formed by the information contained in the DNA and perform a variety of cellular functions. The proteins may be structural (responsible for cell shape and size), or they may be functional like enzymes, signaling intermediates, regulatory proteins, and defense system proteins. However, any kind of genetic defect results in defective protein or alters protein folding which can compromise the functioning of the body and is responsible for the diseases. Figure 1.4 shows the outline of the process of transcription and translation with important steps.

Factors involved in transcription process

It shows the process of transcription and translation. Transcription occurs in the nucleus and requires the usage of three polymerase enzymes. RNApol I for rRNA, pol II for mRNA, and pol III for both rRNA and tRNA. RNApol II initiates the process by associating itself with seven transcription factors, TFIIA, TFIIB, TFIID, TFIIE, TFIIH, and TFIIJ. After the synthesis, preRNA transcript undergoes processing to form mRNA by removal of introns by splicing and polyadenylation and capping. Protein synthesis is initiated by formation of ribosome and initiator tRNA complex to initiation codon (AUG) of mRNA and involves 11 factors. Chain elongation occurs after sequential addition of amino acids by formation of peptide bonds. Then polypeptide can fold or conjugate itself to other biomolecules and may undergo posttranslational modifications as glycosylation or phosphorylation to perform its biological functions

The biotechnological tools are employed toward modification of the gene for gain of function or loss of function of the protein. The technique of removing, adding, or modifying genes in the genome or chromosomes of an organism to bring about the changes in the protein information is called genetic engineering or recombinant DNA technology (Fig. 1.5 ). DNA recombination made possible the sequencing of the human genome and laid the foundation for the nascent fields of bioinformatics, nanomedicine, and individualized therapy. Multicellular organisms like cows, goats, sheep, rats, corn, potato, and tobacco plants have been genetically engineered to produce substances medically useful to humans. Genetic engineering has revolutionized medicine, enabling mass production of safe, pure, more effective versions of biochemicals that the human body produces naturally [ 20 – 22 ].

The process of recombinant DNA technology. The gene of interest from human nucleus is isolated and cloned in a plasmid vector. The gene is ligated with the help of DNA ligase. The vector is transformed into a bacterial host. After appropriate selections, the gene is amplified when bacteria multiply or the gene can be sequenced or the gene can be expressed to produce protein

The technological advancements have resulted in (1) many biopharmaceuticals and vaccines, (2) new and specific ways to diagnose, (3) increasing the productivity and introduction of quality traits in agricultural crops, (4) the ways to tackle the pollutants efficiently for sustainable environmental practices, (5) helped the forensic experts by DNA fingerprinting and profiling, (6) fermentation technology for production of industrially important products. The list is very long with tremendous advancements and products which have boosted the economy of biotechnology sector worldwide [ 16 ]. The biotechnology industry and the products are regulated by various government organizations such as the US Food and Drug Administration (FDA), the Environmental Protection Agency (EPA), and the US Department of Agriculture (USDA).

Medical Biotechnology

This fieldof biotechnology has many applications and is involved in production of recombinant pharmaceuticals, tissue engineering products, regenerative medicines such as stem cell and gene therapy, and many more biotechnology products for better human life (Fig. 1.6 ). Biotechnological tools produce purified bio-therapeutic agents on industrial scales. These include both novel agents and agents formerly available only in small quantities. Crude vaccines were used in antiquity in China, India, and Persia. For example, vaccination with scabs that contained the smallpox virus was a practice in the East for centuries. In 1798 English country doctor Edward Jenner demonstrated that inoculation with pus from sores due to infection by a related cowpox virus could prevent smallpox far less dangerously. It marked the beginning of vaccination. Humans have been benefited incalculably from the implementation of vaccination programs.

Various applications of medical biotechnology

Tremendous progress has been made since the early recombinant DNA technology (RDT) experiments from which the lively—and highly profitable—biotechnology industry emerged. RDT has fomented multiple revolutions in medicine. Safe and improved drugs, accelerated drug discovery, better diagnostic and quick methods for detecting an infection either active or latent, development of new and safe vaccines, and completely novel classes of therapeutics and other medical applications are added feathers in its cap. The technology has revolutionized understanding of diseases as diverse as cystic fibrosis and cancer. Pharmaceutical biotechnology being one of the important sectors involves using animals or hybrids of tumor cells or leukocytes or cells ( prokaryotic, mammalian) to produce safer, more efficacious, and cost-effective versions of conventionally produced biopharmaceuticals. The launch of the new biopharmaceutical or drug requires screening and development. Mice were widely used as research animals for screening. However, in the wake of animal protection, animal cell culture offers accurate and inexpensive source of cells for drug screening and efficacy testing. Pharmaceutical biotechnology’s greatest potential lies in gene therapy and stem cell-based therapy. The underlying cause of defect of many inherited diseases is now located and characterized. Gene therapy is the insertion of the functional gene in place of defective gene into cells to prevent, control, or cure disease. It also involves addition of genes for pro-drug or cytokines to eliminate or suppress the growth of the tumors in cancer treatment.

But the progress so far is viewed by many scientists as only a beginning. They believe that, in the not-so-distant future, the refinement of “targeted therapies” should dramatically improve drug safety and efficacy. The development of predictive technologies may lead to a new era in disease prevention, particularly in some of the world’s rapidly developing economies. Yet the risks cannot be ignored as new developments and discoveries pose new questions, particularly in areas as gene therapy, the ethics of stem cell research, and the misuse of genomic information.

Many bio-therapeutic agents in clinical use are biotech pharmaceuticals. Insulin was among the earliest recombinant drugs. Canadian physiologists Frederick Banting and Charles Best discovered and isolated insulin in 1921. In that time many patients diagnosed with diabetes died within a few years. In the mid-1960s, several groups reported synthesizing the hormone.

The first “bioengineered” drug, a recombinant form of human insulin, was approved by the US Food and Drug Administration (FDA) in 1982. Until then, insulin was obtained from a limited supply of beef or pork pancreas tissue. By inserting the human gene for insulininto bacteria, scientists were able to achieve lifesaving insulinproduction in large quantities. In the near future, patients with diabetes may be able to inhale insulin, eliminating the need for injections. Inhaled insulinproducts like Exubera® were approved by the USFDA; however, it was pulled out and other products like Technosphere® insulin (Afrezza®) are under investigation. They may provide relief from prandial insulin. Afrezza consists of a pre-meal insulinpowder loaded into a cartridge for oral inhalation.

Technosphere technology: The technology allows administration of therapeutics through pulmonary route which otherwise were required to be given as injections. These formulations have broad spectrum of physicochemical characteristics and are prepared with a diverse assortment of drugs with protein or small molecule which may be hydrobhobic or hydrophilic or anionic or cationic in nature. The technology can have its applicability not only through pulmonary route but also for other routes of administration including local lung delivery.

The first recombinant vaccine, approved in 1986, was produced by cloning a gene fragment from the hepatitis B virus into yeast (Merck’s Recombivax HB). The fragment was translated by the yeast’s genetic machinery into an antigenic protein. This was present on the surface of the virus that stimulates the immune response. This avoided the need to extract the antigen from the serum of people infected with hepatitis B.

The Food and Drug administration (FDA) approved more biotech drugs in 1997 than in the previous several years combined. The FDA has approved many recombinant drugs for human health conditions. These include AIDS, anemia, cancers (Kaposi’s sarcoma, leukemia, and colorectal, kidney, and ovarian cancers), certain circulatory problems, certain hereditary disorders (cystic fibrosis, familial hypercholesterolemia, Gaucher’s disease, hemophilia A, severe combined immunodeficiency disease, and Turner’s syndrome), diabetic foot ulcers, diphtheria, genital warts, hepatitis B, hepatitis C, human growth hormone deficiency, and multiple sclerosis. Today there are more than 100 recombinant drugs and vaccines. Because of their efficiency, safety, and relatively low cost, molecular diagnostic tests and recombinant vaccines may have particular relevance for combating long-standing diseases of developing countries, including leishmaniasis (a tropical infection causing fever and lesions) and malaria.

Stem cell research is very promising and holds tremendous potential to treat neurodegenerative disorders, spinal cord injuries, and other conditions related to organ or tissue loss.

DNA analysis is another powerful technique which compares DNA pattern [ 14 ] after performing RFLP and probing it by minisatellite repeat sequence between two or more individuals. Its modification, DNA profiling (process of matching the DNA profiles for STS markers in two or more individuals; see chapter 18), which utilizes multilocus PCR analysis of DNA of suspect and victims, is very powerful and is useful in criminal investigation, paternity disputes, and so many other legal issues. The analysis is very useful in criminal investigations and involves evaluation of DNA from samples of the hair, body fluids, or skin at a crime scene and comparison of these with those obtained from the suspects.

Improved Diagnostic and Therapeutic Capabilities

The sequencing of the human genome in 2003, has given scientists an incredibly rich “parts list” with which to better understand why and how disease happens. It has given added power to gene expression profiling, a method of monitoring expression of thousands of genes simultaneously on a glass slide called a microarray. This technique can predict the aggressiveness of cancer.

The development of monoclonal antibodies in 1975 led to a medical revolution. The body normally produces a wide range of antibodies—the immune system proteins—that defend our body and eliminate microorganisms and other foreign invaders. By fusing antibody-producing cells with myeloma cells, scientists were able to generate antibodies that would, like “magic bullets,” bind with specific targets including unique markers, called antigenic determinants ( epitopes), on the surfaces of inflammatory cells. When tagged with radioisotopes or other contrast agents, monoclonal antibodies can help in detecting the location of cancer cells, thereby improving the precision of surgery and radiation therapy and showing—within 48 h—whether a tumor is responding to chemotherapy.

The polymerase chain reaction, a method for amplifying tiny bits of DNA first described in the mid-1980s, has been crucial to the development of blood tests that can quickly determine exposure to the human immunodeficiency virus (HIV). Genetic testing currently is available for many rare monogenic disorders, such as hemophilia, Duchenne muscular dystrophy, sickle cell anemia, thalassemia, etc.

Another rapidly developing field is proteomics, which deals with analysis and identification of proteins. The analysis is done by two-dimensional gel electrophoresis of the sample and then performing mass spectrometric analysis for each individual protein. The technique may be helpful in detecting the disease-associated protein in the biological sample. They may indicate early signs of disease, even before symptoms appear. One such marker is C-reactive protein, an indicator of inflammatory changes in blood vessel walls that presage atherosclerosis.

Nanomedicine is a rapidly moving field. Scientists are developing a wide variety of nanoparticles and nanodevices, scarcely a millionth of an inch in diameter, to improve detection of cancer, boost immune responses, repair damaged tissue, and thwart atherosclerosis. The FDA has approved a paclitaxel albumin-stabilized nanoparticle formulation (Abraxane® for injectable suspension, made by Abraxis BioScience) for the treatment of metastatic adenocarcinoma of the pancreas. Nanoparticles are being explored in heart patients in the USA as a way to keep their heart arteries open following angioplasty.

Therapeutic proteins are those, which can replace the patients naturally occurring proteins, when levels of the natural proteins are low or absent due to the disease. High-throughput screening, conducted with sophisticated robotic and computer technologies, enables scientists to test tens of thousands of small molecules in a single day for their ability to bind to or modulate the activity of a “target,” such as a receptor for a neurotransmitter in the brain. The goal is to improve the speed and accuracy of therapeutic protein or potential drug discovery while lowering the cost and improving the safety of pharmaceuticals that make it to market.

Many of the molecules utilized for detection also have therapeutic potential too, for example, monoclonal antibodies. The monoclonal antibodies are approved for the treatment of many diseases as cancer, multiple sclerosis, and rheumatoid arthritis. They are currently being tested in patients as potential treatments for asthma, Crohn’s disease, and muscular dystrophy. As the antibodies may be efficiently targeted against a particular cell surface marker, thus they are used to deliver a lethal dose of toxic drug to cancer cells, avoiding collateral damage to nearby normal tissues.

Agricultural Biotechnology

The manhas made tremendous progress in crop improvement in terms of yield; still the ultimate production of crop is less than their full genetic potential. There are many reasons like environmental stresses (weather condition as rain, cold, frost), diseases, pests, and many other factors which reduce the ultimate desired yield affecting crop productivity. The efforts are going on to design crops which may be grown irrespective of their season or can be grown in frost or drought conditions for maximum utilization of land, which would ultimately affect crop productivity [ 24 ]. Agricultural biotechnology aims to introduce sustainable agriculturalpractices with best yield potential and minimal adverse effects on environment (Fig. 1.7 ). For example, combating pests was a major challenge. Thus, the gene from bacterium , the Bt gene, that functions as insect-resistant gene when inserted into crop plants like cotton, corn, and soybean helps prevent the invasion of pathogen, and the tool is called . This management is helpful in reducing usage of potentially dangerous pesticides on the crop. Not only the minimal or low usage of pesticides is beneficial for the crop but also the load of the polluting pesticides on environment is greatly reduced [ 24 ].

Various applications of agricultural biotechnology

Resistance to Infectious Agents Through Genetic Engineering

• The gene comes from the soil bacterium .
• The gene produces crystal proteins called Cry proteins. More than 100 different variants of the Bt toxins have been identified which have different specificity to target insect lepidoptera. For eg., CryIa for butterflies and CRYIII for beetles.
• These Cry proteins are toxic to larvae of insects like tobacco budworm, armyworm, and beetles.
• The Cry proteins exist as an inactive protoxins.
• These are converted into active toxin in alkaline pH of the gut upon solubilization when ingested by the insect.
• After the toxin is activated, it binds to the surface of epithelial cells of midgut and creates pores causing swelling and lysis of cells leading to the death of the insect (larva).
• The genes (cry genes) encoding this protein are isolated from the bacterium and incorporated into several crop plants like cotton, tomato, corn, rice, and soybean.

The proteins encoded by the following cry genes control the pest given against them:

• Cry I Ac and cry II Ab control cotton bollworms.
• Cry I Ab controls corn borer.
• Cry III Ab controls Colorado potato beetle.
• Cry III Bb controls corn rootworm.
• A nematode infects tobacco plants and reduces their yield.
• The specific genes (in the form of cDNA) from the parasite are introduced into the plant using -mediated transformation.
• The genes are introduced in such a way that both sense/coding RNA and antisense RNA (complimentary to the sense/coding RNA) are produced.
• Since these two RNAs are complementary, they form a double-stranded RNA (ds RNA).
• This neutralizes the specific RNA of the nematode, by a process called RNA – interference.
• As a result, the parasite cannot multiply in the transgenic host, and the transgenic plantis protected from the pest.

These resistant crops result in reduced application of pesticides. The yield is high without the pathogen infestations and insecticides. This also helps to reduce load of these toxic chemicals in the environment.

The transformation techniques and their applications are being utilized to develop rice, cassava, and tomato, free of viral diseases by “International Laboratory for Tropical Agricultural Biotechnology” (ILTAB). ILTAB in 1995 reported the first transfer of a resistance gene from a wild-type species of rice to a susceptible cultivated rice variety. The transferred gene expressed and imparted resistance to crop-destroying bacterium Xanthomonas oryzae . The resistant gene was transferred into susceptible rice varieties that are cultivated on more than 24 million hectares around the world [ 6 ].

The recombinant DNA technology reduces the time between the identification of a particular gene to its application for betterment of crops by skipping the labor-intensive and time-consuming conventional breeding [ 3 ]. For example, the alteration of known gene in plant for the improvement of yield or tolerance to adverse environmental conditions or resistance to insect in one generation and its inheritance to further generations. Plant cell and tissue culture techniques are one of the applications where virus-free plants can be grown and multiplied irrespective of their season on large scale (micropropogation), raising haploids, or embryo rescue. It also opens an opportunity to cross two manipulated varieties or two incompatible varieties (protoplast culture) for obtaining best variety for cultivation.

With the help of technology, new, improved, and safe agricultural products may emerge which would be helpful for maintaining contamination-free environment. Biotechnology has the potential to produce:

• High crop yields [ 4 ]
• Crops are engineered to have desirable nutrients and better taste (e.g., tomatoes and other edible crops with increased levels of vitamin C, vitamin E, and/or beta-carotene protect against the risk of some prevalent chronic diseases and rice with increased iron levels protects against anemia)
• Insect- and disease-resistant plants
• Genetic modification avoids nonselective changes
• Longer shelf life of fruits and vegetables

The potential of biotechnology may contribute to increasing agricultural, food, and feed production, protecting the environment, mitigating pollution, sustaining agricultural practices, and improving human and animal health. Some agricultural crops as corn and marine organisms can be potential alternative for biofuel production. The by-products of the process may be processed to produce other chemical feedstocks for various products. It is estimated that the world’s chemical and fuel demand could be supplied by such renewable resources in the first half of the next century [ 5 ].

Food Biotechnology

Food biotechnology is an emerging field, which can increase the production of food, improving its nutritional content and improving the taste of the food. The food is safe and beneficial as it needs fewer pesticides and insecticides. The technology aims to produce foods which have more flavors, contain more vitamins and minerals, and absorb less fat when cooked. Food biotechnology may remove allergens and toxic components from foods, for their better utility [ 6 , 7 ].

Environmental Biotechnology

Environmental biotechnology grossly deals with maintenanceof environment, which is pollution-free, the water is contamination-free, and the atmosphere is free of toxic gases. Thus, it deals with waste treatment, monitoring of environmental changes, and pollution prevention. Bioremediation in which utilization of higher living organisms (plants: phytoremediation) or certain microbial species for decontamination or conversion of harmful products is done is the main application of environmental biotechnology. The enzyme bioreactors are also being developed which would pretreat some industrial and food waste components and allow their removal through the sewage system rather than through solid waste disposal mechanisms. The production of biofuel from waste can solve the fuel crisis (biogas). Microbes may be engineered to produce enzymes required for conversion of plant and vegetable materials into building blocks for biodegradable plastics. In some cases, the by-products of the pollution-fighting microorganisms are themselves useful. For example, methane can be derived from a form of bacteria that degrades sulfur liquor, a waste product of paper manufacturing. This methane thus obtained is used as a fuel or in other industrial processes. Insect- and pest-resistant crops have reduced the use and environmental load of insecticides and pesticides. Insect-protected crops allow for less potential exposure of farmers and groundwater to chemical residues while providing farmers with season-long control.

Industrial Biotechnology

The utilizationof biotechnological tools (bioprocessing) for the manufacturing of biotechnology-derived products (fuels, plastics, enzymes, chemicals, and many more compounds) on industrial scale is industrial biotechnology. The aim is to develop newer industrial manufacturing processes and products, which are economical and better than preexisting ones with minimal environmental impact. In industrial biotechnology, (1) microorganisms are being explored for producing material goods like fermentation products as cheese; (2) biorefineries where oils, sugars, and biomass may be converted into biofuels, bioplastics, and biopolymers; (3) and value-added chemicals from biomass. The utilization of modern techniques can improve the efficiency and reduces the environmental impacts of industrial processes like textile, paper, pulp, and chemical manufacturing. For example, development and usage of biocatalysts, such as enzymes, to synthesize chemicals and development of antibiotics and better tasting liquors and their usage in food industry have provided safe and effective processing for sustainable productions. Biotechnological tools in the textile industry are utilized for the finishing of fabrics and garments. Biotechnology also produces spider silk and biotech-derived cotton that is warmer and stronger and has improved dye uptake and retention, enhanced absorbency, and wrinkle and shrink resistance.

Biofuels may be derived from photosynthetic organisms, which capture solar energy, transform it in other products like carbohydrates and oils, and store them. Different plants can be used for fuel production:

• Bioethanol can be obtained from sugar (as sugarcane or sugar beet) or starch (like corn or maize). These are fermented to produce ethanol, a liquid fuel commonly used for transportation.
• Biodiesel can be obtained from natural oils from plants like oil palm, soybean, or algae. They can be burned directly in a diesel engine or a furnace, or blended with petroleum, to produce fuels such as biodiesel.
• Wood and its by-products can be converted into liquid biofuels, such as methanol or ethanol, or into wood gas. Wood can also be burned as solid fuel, like the irewood.

In these kinds of biological reaction, there are many renewable chemicals of economic importance coproduced as side streams of bioenergy and biofuels as levulinic acid, itaconic acid, and sorbitol. These have tremendous economic potential and their fruitful usage would depend upon the collaboration for research and development between the government and the private sector.

Enzyme Production

The enzymeshave big commercial and industrial significance. They have wide applications in food industry, leather industry, pharmaceuticals, chemicals, detergents, and research. In detergents the alkaline protease, subtilisin (from Bacillus subtilis ), was used by Novo Industries, Denmark. The production of enzymes is an important industrial application with world market of approximately 5 billion dollars. The enzymes can be obtained from animals, plants, or microorganisms. The production from microorganisms is preferred as they are easy to maintain in culture with simple media requirements and easy scale-up. The important enzymes for the industrial applications are in food industry, human application, and research. A few animal enzymes are also important as a group of proteolytic enzymes, for example, plasminogen activators, which act on inactive plasminogen and activate it to plasmin, which destroys fibrin network of blood clot. Some of the plasminogen activators are urokinase and tissue plasminogen activators (t-PA). Urokinase (from urine) is difficult to obtain in ample quantity; thus, t-PA is obtained from cells grown in culture medium. Streptokinase (bacterial enzyme) is also a plasminogen activator but is nonspecific and immunogenic.

Enzyme engineering is also being tried where modifications of specific amino acid residue are done for improving the enzyme properties. One of the enzymes chymosin (rennin) coagulates milk for cheese manufacturing.

The enzymes can be produced by culturing cells, growing them with appropriate substrates in culture conditions. After optimum time the enzymes may be obtained by cell disruption (enzymatic/freeze–thaw/osmotic shock) followed by preparative steps (centrifugation, filtration), purification, and analysis. The product is then packaged and ultimately launched in the market.

After their production, they can be immobilized on large range of materials (agar, cellulose, porous glass, or porous alumina) for subsequent reuse. Some of the important industrial enzymes are α-amylase (used for starch hydrolysis), amyloglucosidase (dextrin hydrolysis), β-galactosidase (lactose hydrolysis), aminoacylase (hydrolysis of acylated L-amino acids), glucose oxidase (oxidation of glucose), and luciferase (bioluminescence). Some of the medically important enzymes are urokinase and t-PA for blood clot removal and L-asparaginase for removal of L-asparagine essential for tumor growth and thus used for cancer chemotherapy in leukemia.

Exploring Algae for Production of Biofuels

The energyrequirement of present population is increasing and gradually fossil fuels are rapidly depleting. Thus, renewable energy sources like solar energy and wind-, hydro-, and biomass-based energy are being explored worldwide. One of the feedstocks may be microalgae, which are fast-growing, photosynthetic organisms requiring carbon dioxide, some nutrients, and water for its growth. They produce large amount of lipids and carbohydrates, which can be processed into different biofuels and commercially important coproducts. The production of biofuels using algal biomass is advantageous as they (1) can grow throughout the year and thus their productivity is higher than other oil seed crops, (2) have high tolerance to high carbon dioxide content, (3) utilize less water, (4) do not require herbicides or pesticides with high growth potential (waste water can be utilized for algal cultivation), (5) can sustain harsh atmospheric conditions, and (6) do not interfere with productivity of conventional crops as they do not require agricultural land. The production of various biofuels from algae is schematically represented in Fig. 1.8 .

Different biofuel productions by using microalgae. The algae use sunlight, CO2, water, and some nutrients

Algae can serve as potential source for biofuel production; however, biomass production is low. The production has certain limitations, as cultivation cost is high with requirement of high energy [ 1 ].

Marine or Aquatic Biotechnology

Marine or aquatic biotechnology also referred to as “blue biotechnology” deals with exploring and utilizing the marine resources of the world. Aquatic or marine life has been intriguing and a source of livelihood for many since years. As major part of earth is acquired by water, thus nearly 75–80 % types of life forms exist in oceans and aquatic systems. It studies the wide diversity found in the structure and physiology of marine organisms. They are unique in their own ways and lack their equivalent on land. These organisms have been explored and utilized for numerous applications as searching new treatment for cancer or exploring other marine resources, because of which the field is gradually gaining momentum and economic opportunities [ 19 ]. The global economic benefits are estimated to be very high. The field aims to:

• Fulfill the increasing food supply needs
• Identify and isolate important compounds which may benefit health of humans
• Manipulate the existing traits in sea animals for their improvement
• Protect marine ecosystem and gain knowledge about the geochemical processes occurring in oceans

Some of the major applications are discussed:

• Aquaculture: Aquaculture refers to the growth of aquatic organisms in culture condition for commercial purposes. These animals may be shellfish, finfish, and many others. Mariculture refers to the cultivation of marine animals. Their main applications are in food, food ingredients, pharmaceuticals, and fuels, the products are in high demand, and various industries are in aquaculture business, for example, crawfish farming (Louisiana), catfish industry (Alabama and Mississippi Delta), and trout farming (Idaho and West Virginia).
• Transgenic species of salmon with growth hormone gene has accelerated growth of salmons.
• Molt-inhibiting (MIH) from blue crabs leads to soft-shelled crab.
• : Anovel protein antifreeze protein (AFP) was identified. AFPs were isolated from Northern cod (bottom-dwelling fish) living at the Eastern Canada coast and teleosts living in extremely cold weather of Antarctica. AFPs have been isolated from Osmerus mordax (smelt), Clupea harengus (herring), Pleuronectes americanus (winter flounder), and many others. Due to antifreeze properties (lowering the minimal freezing temperature by 2–3 °C), the gene has potential for raising plants which are cold tolerant (e.g., tomatoes).
• Medicinal applications : For osteoporosis, salmon calcitonin (calcitonin is thyroid hormone promoting calcium uptake and bone calcification) with 20 times higher bioactivity is available as injection and nasal spray.
• Hydroxyapatite ( HA ): Obtained from coral reefs and is an important component of bone and cartilage matrix. Its implants are prepared by Interpore Internationals which may be used for filling gaps in fractured bones.

Many anti-inflammatory, analgesic, anticancerous compounds have been identified from sea organisms which can have tremendous potential for human health.

Tetrodotoxin (TTX) is the most toxic poison (10,000 times more lethal than cyanide) produced by Japanese pufferfish or blowfish ( Fugu rubripes ). TTX is being used to study and understand its effect on sodium channels which can help guide the development of drugs with anesthetic and analgesic properties.

Other Products

• Taq polymerase from Thermus aquaticus which is used in PCR reactions and obtained from hot spring Archaea.
• Collagenase (protease) obtained from Vibrio is used in tissue engineering and culturing.

Transgenic Animals and Plants

In the early1980s, inserting DNA from humans into mice and other animals became possible. The animals and plants which have foreign gene in each of their cells are referred to as transgenic organisms and the inserted gene as transgene. Expression of human genes in these transgenic animals can be useful in studies, as models for the development of diabetes, atherosclerosis, and Alzheimer’s disease. They also can generate large quantities of potentially therapeutic human proteins. Transgenic plants also offer many economic, safe, and practical solutions for production of variety of biopharmaceuticals. The plants have been engineered to produce many blood products (human serum albumin, cytokines), human growth hormone, recombinant antibodies, and subunitvaccines.

The usage of transgenic plants for the production of recombinant pharmaceuticals might open new avenues in biotechnology. As plants can be grown inexpensively with minimal complicated requirements, thus they may have tremendous therapeutic potential. The plants have been engineered to produce more nutrients or better shelf life. The transgenic plants have been created which have genes for insect resistance (Bt cotton, soybean, corn). Now billion acres of land is used for cultivation of genetically engineered crops of cotton, corn, and soybean as they have higher yield and are pest resistant. However, due to social, ethical, and biosafety issues, they have received acceptance as well as rejections at many places and health and environment-related concerns in many parts of the world [ 8 ].

Response to Antibiotic Resistance

Antibiotics areone of the broadly used therapeutic molecules produced by certain classes of microorganisms (bacteria and fungi) which can be used in diverse clinical situations to eliminate bacteria, improve symptoms, and prevent number of infections. Antibiotics have various other applications apart from clinical aspects. They can be used for the treatment of tumors and treatment of meat, in cattles and livestocks, in basic biotechnological work. However, their effectiveness is a matter of concern as bacteria which are continuously exposed to certain antibiotics might become resistant to it due to accumulation of mutations. These days antibiotic-resistant bacteria have increased and some of them have developed multiple drug resistance. Thus, it has become very difficult to initiate therapy in diseases like tuberculosis and leprosy. Biotechnology is solving the urgent and growing problem of antibiotic resistance. With the help of bioinformatics—powerful computer programs capable of analyzing billions of bits of genomicsequence data—scientists are cracking the genetic codes of bacteria and discovering “weak spots” vulnerable to attack by compounds identified via high-throughput screening. This kind of work led in 2000 to the approval of Zyvox (linezolid), an antibiotic to reach the market in 35 years.

Lytic bacteriophage viruses that infect and kill bacteria may be another way to counter resistance. First used to treat infection in the 1920s, “phage therapy” was largely eclipsed by the development of antibiotics. However, researchers in the former Soviet Republic of Georgia reported that a biodegradable polymer impregnated with bacteriophages and the antibiotic Cipro successfully healed wounds infected with a drug-resistant bacterium.

After exposure of strontium-90, three Georgian lumberjacks from village Lia had systemic effects, and two of them developed severe local radiation injuries which subsequently became infected with Staphylococcus aureus . Upon hospitalization, the patients were treated with various medications, including antibiotics and topical ointments; however, wound healing was only moderately successful, and their S. aureus infection could not be eliminated. Approximately 1 month after hospitalization, treatment with PhagoBioDerm (a wound-healing preparation consisting of a biodegradable polymer impregnated with ciprofloxacin and bacteriophages) was initiated. Purulent drainage stopped within 2–7 days. Clinical improvement was associated with rapid (7 days) elimination of the etiologic agent, and a strain of S. aureus responsible for infection was resistant to many antibiotics (including ciprofloxacin) but was susceptible to the bacteriophages contained in the PhagoBioDerm preparation [ 11 ].

The Challenges for the Technology

Gene therapy.

Some biotechapproaches to better health have proven to be more challenging than others. An example is gene transfer, where the defective gene is replaced with a normally functioning one. The normal gene is delivered to target tissues in most cases by virus that is genetically altered to render it harmless. The first ex vivo gene transfer experiment, conducted in 1990 at the National Institutes of Health (NIH), on Ashanti DeSilva who was suffering from severe combined immunodeficiency (SCID) helped boost her immune response and successfully corrected an enzyme deficiency. However, treatment was required every few months. However, 9 years later, a major setback occurred in gene therapy trial after the death of 18-year-old Jesse Gelsinger suffering from ornithine transcarbamylase (OTC) deficiency due to intense inflammatory responses followed by gene therapy treatment. There were some positive experiences and some setbacks from gene therapy trials leading to stricter safety requirements in clinical trials.

Designer Babies

The fancyterm designer baby was invented by media. Many people in society prefer embryos with better traits, intellect, and intelligence. They want to select embryo post germline engineering. This technique is still in infancy but is capable of creating lot of differences in the society thus requires appropriate guidelines.

Genetically Modified Food

Genetically modifiedcrops harboring genes for insect resistance were grown on billion of acres of land. These crops became very popular due to high yield and pest resistance. However, some of the pests gradually developed resistance for a few of these transgenic crops posing resistant pest threat. The other technologies as “traitor” and “terminator” technologies pose serious risk on crop biodiversity and would impart negative characters in the crop (they were not released due to public outcry).

Pharmacogenomics

Scientists do not believe they will find a single gene for every disease. As a result, they are studyingrelationships between genes and probing populations for variations in the genetic code, called single nucleotide polymorphisms, or SNPs, that may increase one’s risk for a particular disease or determine one’s response to a given medication. This powerful ability to assign risk and response to genetic variations is fueling the movement toward “individualized medicine.” The goal is prevention, earlier diagnosis, and more effective therapy by prescribing interventions that match patients’ particular genetic characteristics.

Tissue Engineering

Tissue engineering is one of the emerging fields with tremendous potential to supply replacement tissue and organ option for many diseases. Lot is achieved, lot more need to be achieved.

Ethical Issues

The pursuit of cutting-edge research “brings us closer to our ultimate goal of eliminating disability and disease through the best care which modern medicine can provide.” Understanding of the genetics of heart disease and cancer will aid the development of screening tools and interventions that can help prevent the spread of these devastating disorders into the world’s most rapidly developing economies.

Biotechnology is a neutral tool; nevertheless, its capabilities raise troubling ethical questions. Should prospective parents be allowed to “engineer” the physical characteristics of their embryos? Should science tinker with the human germ line, or would that alter in profound and irrevocable ways what it means to be human?

More immediately, shouldn’t researchers apply biotechnology—if they can—to eliminate health disparities among racial and ethnic groups? While genetic variation is one of many factors contributing to differences in health outcome (others include environment, socioeconomic status, health-care access, stress, and behavior), the growing ability to mine DNA databases from diverse populations should enable scientists to parse the roles these and other factors play.

Biotechnology along with supportive health-care infrastructure can solve complicated health problems. Accessibility to the new screening tests, vaccines, and medications and cultural, economic, and political barriers to change must be overcome. Research must include more people from disadvantaged groups, which will require overcoming long-held concerns, some of them have had about medical science.

Biotechnology has been a significant force which has improved the quality of lives and has incalculably benefitted human beings. However, technology does have prospects of doing harm also due to unanticipated consequences. Each technology is subjected to ethical assessment and requires a different ethical approach. Obviously the changes are necessary as technology can have major impact on the world; thus, a righteous approach should be followed. There is uncertainty in predicting consequences, as this powerful technology has potential to manipulate humans themselves. Ethical concerns are even more important as the future of humanity can change which require careful attention and consideration. Therefore, wisdom is required to articulate our responsibilities toward environment, animals, nature, and ourselves for the coming future generations. We need to differentiate what is important technologically rather that what technology can do. For an imperative question, that is, whether this can be achieved, the research must answer “Why should it be achieved”? Who would it benefit?

Issues Related to Safety

• As the new GM crops are entering the market, the issue regarding their consumption, whether they are safe, without any risk, is one of the important concerns [ 2 ]. Though the results related to safety and usage are well reported (as compared to conventional crops), unknown fear from these products makes them non acceptable at many places [ 20 ].
• As insect- and pest-resistant varieties are being prepared and used as Bt genes in corn and cotton crops, there exists a risk of development of resistance insect population. Another important factor is that these resistant crops may harm other species like birds and butterfly.
• The development of more weeds may occur as cross-pollination might result in production of weeds with herbicide resistance which would be difficult to control.
• The gene transfers might cross the natural species boundary and affect biological diversity.
• The judgment of their usage would depend upon the clear understanding of risks associated with safety of these products in determining the impact of these on environment, other crops, and other animal species.

Future of the Technology

With the understanding of science, we should understand that genetic transfers have been occurring in animals and plant systems; thus, the risk of the biotechnology-derived products is similar as conventional crops [ 12 ].

The biotechnology products would be acceptable to many if they are beneficial and safe. People are willing to buy crops free of pesticides and insecticides. Nowadays people are also accepting crops grown without the usage of chemical fertilizers or pesticides, which are high in nutritive values.

The labeling of the product is also an ethical issue as some believe that labeling any product as biotechnology product might be taken by consumer as warning signs; however, others believe that labeling should be done as consumer has every right to know what he is consuming [ 9 ]. The products may be acceptable if consumers can accept the food derived from biotechnology weighing all pros and cons and, if the price is right, has more nutritive values, is good in taste, and is safe to consume [ 10 ].

Biotechnology is at the crossroads in terms of fears and thus public acceptance [ 15 ]. Surprisingly the therapeutic products are all accepted and find major place in biopharmaceutical industry, but food crops are still facing problems in worldwide acceptance. The future of the world food supply depends upon how well scientists, government, and the food industry are able to communicate with consumers about the benefits and safety of the technology [ 13 , 16 ]. Several major initiatives are under way to strengthen the regulatory process and to communicate more effectively with consumers by conducting educational programs [ 18 , 23 ].

Chapter End Summary

• The advantages of biotechnology are so broad that it is finding its place in virtually every industry. It has applications in areas as diverse as pharmaceuticals, diagnostics, textiles, aquaculture, forestry, chemicals, household products, environmental cleanup, food processing, and forensics to name a few.
• Biotechnology is enabling these industries to make new or better products, often with greater speed, efficiency, and flexibility.
• With the applications of recombinant DNA technology, more safer and therapeutic drugs are produced. These recombinant products do not elicit unwanted immunological response which is observed when the product is obtained from other live or dead sources. Many of these therapeutics are approved for human usage, and many of them are in the phase of development.
• Immunological and DNA-based techniques like PCR (polymerase chain reaction) are used for early diagnosis of disorders. PCR and NAAT with microarray can be utilized for the diagnosis of many diseases, and it can detect mutations in gene.
• The technology holds promise through stem cell research and gene therapy and holds applications in forensic medicine.
• The technique may be helpful in developing useful and beneficial plants. It overcomes the limitations of traditional plant breeding. The techniques of plant tissue culture, transgenics, and marker-assisted selections are largely used for selecting better yielding varieties and imparting quality traits in plants.
• Food industries. Production of single-cell protein, spirulina, enzymes, and solid-state fermentations
• Increase and improvement of agricultural production
• Production of therapeutic pharmaceuticals
• Production of vaccines and monoclonal antibodies
• Cultivation of virus for vaccine production

Multiple Choice Questions

• All of the above
• Vitamin D and calcium
• Growth hormone
• Tissue plasminogen activator
• Factor VIII
• Genetically modifying organism
• Production of therapeutics
• Production of better diagnosis
• Increase in yield of crops
• Improved crop varieties
• Lesser fertilizers and agrochemicals
• All of these
• It is resistant to it.
• The toxin is enclosed in vesicle.
• The toxin is present in inactive form.
• None of these.
• Gene therapy
• Replacement protein therapy
• Stem cell therapy
• The productivity would improve.
• The usage of chemical agent would be reduced.
• The environment and crop would be insecticide free.
• All of the above.
• Detoxifying waste material
• Burying waste material
• Burning waste material
• None of these

(1) In all the cells of our body, all the genes are active.

(2) In different cells of our body, different genes are active.

(3) Gene expression is spatially and temporally regulated.

• All 1, 2, and 3 are correct.
• 1 and 2 are correct.
• 1 and 3 are correct.
• 2 and 3 are correct.
• Inoculation with monoclonal antibody was able to prevent small pox.
• Inoculation with pus from sores due to cowpox could prevent small pox.
• Attenuated vaccine was able to prevent small pox.
• None of the above.
• 1. (c); 2. (a); 3. (c); 4. (d); 5. (d); 6. (d); 7. (c); 8. (a); 9. (d); 10. (a); 11. (d); 12. (b)

Review Questions

• Q1. What are cry proteins? What is their importance?
• Q2. Give some applications of biotechnology in agriculture.
• Q3. What is your opinion about labeling of biotechnology-based food product as rDNA technology derived product?
• Q4. What are applications of biotechnology in maintaining environment?
• Q5. What is medical biotechnology?
• Q6. What are the challenges faced by biotechnology industry?
• Q7. What do you think about GM crops?

Some Related Resources

• http://ificinfo.health.org/backgrnd/BKGR14.htm
• http://www.bio.org/aboutbio/guide1.html
• http://www.bio.org/aboutbio/guide2000/guide00_toc.html
• http://www.bio.org/aboutbio/guide3.html
• http://www.bio.org/aboutbio/guide4.html
• http://www.dec.ny.gov/energy/44157.html
• http://www.ers.usda.gov/whatsnew/issues/biotech/define.htm
• http://www.nal.usda.gov/bic/bio21
• http://www.nature.com/nbt/press_release/nbt1199.html
• www.angelfire.com/scary/intern/links.html
• www.bio-link.org/library.htm
• www.biospace.com
• www.dnai.org
• www.fiercebiotech.com
• www.iastate.edu
• www.icgeb.trieste.it
• www.ncbi.nlm.nih.gov

• Open access
• Published: 15 July 2022

Bioinformatics approaches and applications in plant biotechnology

• Yung Cheng Tan 1 ,
• Asqwin Uthaya Kumar   ORCID: orcid.org/0000-0002-8785-6260 1 , 2 ,
• Ying Pei Wong 1 &
• Anna Pick Kiong Ling   ORCID: orcid.org/0000-0003-0930-0619 1  

Journal of Genetic Engineering and Biotechnology volume  20 , Article number:  106 ( 2022 ) Cite this article

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In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage and management of data, and the development of software for analysis, visualization, modelling, and prediction of large data set.

Particularly in plant biotechnology, the amount of information has multiplied exponentially with a large number of databases available from many individual plant species. Efficient bioinformatics tools and methodologies are also developed to allow rapid genome sequence and the study of plant genome in the ‘omics’ approach. This review focuses on the various bioinformatic applications in plant biotechnology, and their advantages in improving the outcome in agriculture. The challenges or limitations faced in plant biotechnology in the aspect of bioinformatics approach that explained the low progression in plant genomics than in animal genomics are also reviewed and assessed.

There is a critical need for effective bioinformatic tools, which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant’s genome. The advancement in bioinformatics is not only beneficial to the field of plant biotechnology and agriculture sectors, but will also contribute enormously to the future of humanity.

Over the past decades, the term ‘bioinformatics’ has become a buzzword in all areas of research in biological science. With the continuous development and advancement in molecular biology, the explosive growth of biological information required a more organized, computerized system to collect, store, manage, and analyse the vast amount of biological data generated in the experiments from all fields [ 1 ]. Bioinformatics, as a new emerging interdisciplinary field for the past few decades, has many tools and techniques that are essential for efficient sorting and organizing of biological data into databases [ 1 , 2 ]. Bioinformatics can be referred as a computer-based scientific field which applies mathematics, biology, and computer science to form into a single discipline for the analyses and interpretation of genomics and proteomics data [ 2 , 3 ]. In short, the main components of bioinformatics are (a) the collection and analysis of database and (b) the development of software tools and algorithm as a tool for interpretation of biological data [ 2 ]. Bioinformatics played a crucial role in many areas of biology as its applications provide various types of data, including nucleotide and amino acid sequences, protein domains and structure as well as expression patterns from various organisms [ 3 ]. Similarly, the field of plant biotechnology has also taken advantages of bioinformatics, which provides full genomic information of various plant species to allow for efficient exploration into plants as biological resource to humans [ 1 , 3 , 4 ]. The intention of this article is to describe some of the key concepts, tools, and its applications in bioinformatics that are relevant to plant biotechnologies. The current challenges and limitations for improvement and continuous development of bioinformatics in plant science are also described.

Applications of bioinformatics in plant biotechnology

The introduction of bioinformatics and computational biology into the area of plant biology is drastically accelerating scientific invention in life science. With the aid of sequencing technology, scientists in plant biology have revealed the genetic architecture of various plant and microorganism species, such as proteome, transcriptome, metabolome, and even their metabolic pathway [ 1 ]. Sequence analysis is the most fundamental approach to obtain the whole genome sequence such as DNA, RNA, and protein sequence from an organism’s genome in modern science. The sequencing of whole genome permits the determination of organization of different species and provides a starting point to understand their functionality. A complete sequence data consists of coding and non-coding regions, which can act as a necessary precursor for any functional gene that determines the unique traits possessed by organisms. The resulting sequence includes all regions such as exons, introns, regulator, and promoter, which often leads to a vastly large amount of genome information [ 5 ]. With the emergence of next-generation sequencing (NGS) and some other omics technologies used to examine plants genomics, more and more sequenced plants genome will be revealed [ 1 , 6 , 7 , 8 ]. To deal with these vast amounts of data, the development and implementation of bioinformatics allow scientists to capture, store, and organize them in a systematic database [ 1 , 5 ].

Bioinformatics databases and tools for plant biotechnology

In the field of bioinformatics, there are a variety of options of databases and tools that are available to perform analysis related to plant biotechnology. Next-generation sequencing (NGS) and bioinformatics analysis on the plant genomes over the years have generated a large amount of data. All these data are submitted to various and multiple databases that are publicly available online. Each database is unique and has its focus. For instance, CottonGen, database is solely dedicated to obtaining genomics and breeding information of any cotton species of interest [ 9 ]. The establishment of such database eases the researchers who are working on cotton genomic studies by focussing on using just one database instead of searching through other available databases. However, some databases are established and designed to cater not only to one specific species or genus, but focus on all the plant species, such as the National Center for Biotechnology Information (NCBI) ( https://www.ncbi.nlm.nih.gov/ ) database, which as of 2021 possesses almost 21,000 plant genomes that are available for access [ 10 ]. Such a database is useful for studies that do not focus on one specific genus or species. This eases the researchers in accessing to all kinds of genomic data in one database. This section will briefly discuss some of the available plant genome databases, which are publicly accessible and not designated for one genus or species alone.

First would be the globally known and recognized database by all the researchers and biologists, which is the NCBI database. NCBI has been dedicated for gathering and analysing information about molecular biology, biochemistry, and genetics. In the NCBI database, one can download the genome information of the plant species of interest from either gene expression omnibus (GEO) ( https://www.ncbi.nlm.nih.gov/geo/ ) or sequence read archive (SRA) ( https://www.ncbi.nlm.nih.gov/sra ) by simply stating the scientific name of the plant in the search bar and the entire genomic information of the plant can then be obtained. The GEO and SRA comprise processed or raw gene expression data or RNA sequencing of plants that are reposited in the repository. For instance, to obtain the genomics of Rosa chinensis (Rose plant), by inputting the name in the search bar, it will direct to the search result page where the researcher can select the most recent or suitable datasets with specific accession number. Depending on the profiling platform used in each dataset, researchers could retrieve either gene symbols, Ensemble ID, open reading frame, chromosomal location, regulatory elements, etc. The information allows researcher to further analyse the subject of study using bioinformatics tools such as gene ontology ( http://geneontology.org/ ), Database for Annotation, Visualization and integration Discovery (DAVID) ( https://david.ncifcrf.gov/ ), Basic Local Alignment Search Tool (BLAST) ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ), and others that is relevant for the study.

Another database that is available for accessing plant genome database is EnsemblPlants ( https://plants.ensembl.org/index.html ). Unlike the NCBI database, which is not only dedicated to plant genomes, EnsemblPlants is specifically dedicated to accessing plant genomes. EnsemblPlant is part of the Ensembl project that started in 1999, where the project aimed to automatically annotate the genome and integrate the outcome of the annotation with other publicly available biological data and establish an open access archive or database online for the use of the research community [ 11 ]. Ensembl project later launched the taxonomic specific websites designated for each taxon under their project that also includes the plants. The database is a user-friendly integrative platform, where it is continuously updated with the new addition of plant species every time a plant genome is completely sequenced. Compared to the NCBI database mentioned earlier, EnsemblPlant not only provides genome sequence, gene models, and functional annotation of the plant species of interest, but also includes the polymorphic loci, population structure, genotype, linkage, and phenotype information [ 11 , 12 ]. Unlike, NCBI, EnsemblPlant does also provide comparative genomics data of the plant species of interest. This indicates that the platform does not only offer genome sequence data but provide additional analytical data about the plant species of interest and help the researchers who are working on plant bioinformatics to save a lot of time by reducing the tedious work in running the analysis. Yet, the researchers could re-assess the data if necessary, depending on the stringency of their work.

Aside from the abovementioned databases that are widely used for retrieving plant genome sequence, there are still other plant databases such as PlantGDB, MaizeDIG, and Phytozome that can also be considered. Table 1 lists the available database and tools that are widely applied in plant biotechnology.

Biotechnology and bioinformatics for plant breeding

Plant breeding can be defined as the changing or improvement of desired traits in plants to produce improved new crop cultivars for the benefits of humankind [ 8 ]. Jhansi and Usha [ 13 ] mentioned a few benefits brought by genetically engineered plants such as improved quality, enhanced nutritional value, and maximized yield. The revolution of life science in molecular biology and genomics has enabled the leaps forward in plant breeding by applying the knowledge and biological data obtained in genomics research on crops [ 6 , 8 , 13 ]. In modern agriculture, transgenic technology on plants refers to genetic modification, which is done on plants or crops by altering or introducing foreign genes into the plant, to make them useful and productive and enhance their characteristic [ 13 , 14 ]. As mentioned above, the evolution of next-generation sequencing (NGS) and other sequencing technologies produces a large size of biological data which require databases to store the information. The accessibility of whole genome sequences in databases allows free association across genomes with respect to gene sequence, putative function, or genetic map position. With the aid of software, it is possible to formulate predictive hypothesis and incorporate the desired phenotypes from a complex combination into plants by looking at those genetic markers which score well and gives a higher reliability in breeding [ 2 , 15 ]. Other than genome sequence information, databases which store the information of metabolites also play a crucial role in the study of interaction with proteomics and genomics to reflect the changes in phenotype and specific function of an organism [ 1 ]. Some of the most widely used metabolomics databases for plants and crops such as Metlin ( http://metlin.scripps.edu ), provides multiple metabolite searching and about 240,000 metabolites, nearly 72,000 high-resolution MS/MS spectra, and PlantCyc ( https://plantcyc.org/ ), a database which stores information about biochemical pathway and their catalytic enzyme and genes from plants [ 1 , 16 ]. Moreover, single-nucleotide polymorphism markers also benefit from the revolution of NGS and other sequencing technologies. By using NGS, RNA sequencing (RNA-seq) allows direct measure of mRNA profile in order to identify known single-nucleotide polymorphism (SNP) [ 1 ]. SNP is the unique allelic variation within a genome of same species, which can be used as biological markers to locate the genes associated with desired traits in plants [ 17 , 18 ]. Besides, transcriptome resequencing using NGS allows rapid and inexpensive SNP discovery within a large, complex gene with highly repetitive regions of a genome such as wheat, maize, sugarcane, avocado, and black currant [ 17 ]. Figure 1 illustrates briefly the process involved in plant breeding using NGS and bioinformatics.

Brief process of plant breeding involving NGS and bioinformatics

Ever since the first transgenic rice production in 2000, there has been a significant revolution in crop genome sequencing projects, along with the advancement in technologies, rapidly increasing the pace in genetically modified organism (GMO) [ 2 , 13 , 19 ]. Among all the products in rice biotechnology, one of the most widely known GM rice is golden rice. Golden rice is a variety of rice engineered by introducing the biosynthetic pathway to produce β-carotene (pro-vitamin A) into staple food in order to resolve vitamin A deficiency. The World Health Organization has classified vitamin A deficiency as public health problem as it causes half a million of children to childhood blindness [ 13 ]. Vitamin A is an essential nutrient to humans as it helps with development of vision, growth, cellular differentiation, and proliferation of immune system; insufficient intake of vitamin A may lead to childhood blindness, anaemia, and reduced immune responsiveness against infection [ 20 ]. Being the first crop genome to be sequenced, rice has become the most suitable model to initiate the development and improvement of other species in genomic aspect [ 21 , 22 , 23 , 24 ]. The particular reason is due to its small genome size and diploidy, which enables rice to be an excellent model for other cereal crops with larger genomes, such as maize and wheat [ 21 , 23 ]. Song et al. [ 22 ] reported the complete genome sequence of two rice subspecies, japonica and indica , in 2005 that laid a strong foundation for molecular studies and plant breeding research [ 22 , 24 ]. With recent advancement in bioinformatics, it is now possible to run the sequence alignment between large and complex genome from other crop species with genomic data available from rice, by using different software or tools, in order to find out the shared conserved sequence through comparative genomics [ 2 , 7 ]. Vassilev et al. stated some of the most commonly used programmes such as BLAST and FASTA format allowed rapid sequence searching in databases and give the best possible alignment to each sequence [ 25 ]. The programming algorithm calculates the alignment score to measure the proportion of homology matching residue between sequence from related species [ 2 ].

Wheat, as the most widely grown consumed crops, together with rice and maize contributes more than 60% of the calories and protein for our daily life [ 26 , 27 ]. To meet the demands of human population growth, it is necessary to achieve more understanding in wheat research and breeding in order to accelerate the production of wheat yield by 2050 [ 26 , 27 , 28 ]. Despite its importance, the improvement of wheat has been challenging as the researchers have to overcome the complexity of the wheat genome such as highly repetitive and large polyploid in order to get a fully sequenced reference genome [ 26 , 29 ]. Advances in next-generation sequencing (NGS) platforms and other bioinformatics tools have revealed the extensive structural rearrangements and complex gene content in wheat, which revolutionized wheat genomics with the improvement of wheat yield and its adaptation to diversed environments [ 26 , 29 ]. The NGS platforms allow the swift detection of DNA markers from the huge genome data in a short period of time. These NGS-based approaches have undoubtedly revolutionized the allele discovery and genotype-by-sequencing (GBS). By providing a high-quality reference genome of wheat in databases, it allows more sequence comparison between wheat and other species to find out more homologous gene. Moreover, the development of sequencing technologies in both high-throughput genotyping and read length, combining with biological databases, allow the rapid development of novel algorithm to complex wheat genome [ 29 , 30 ]. For instance, genome-wide association studies (GWAS) are an approach used in genome research which allows rapid screening of raw data to select specific regions with agronomic traits [ 29 , 31 ]. It allows multiple genetic variants across genome to be tested to study the genotype-phenotype association; thus, this method can be used to facilitate improvement in crop breeding via genomic selection and genetic modification [ 16 , 29 ].

Maize, a globally important crop, not only has a wide variety of uses in terms of economic impact, but can also serve as genetic model species in genotype to phenotype relationship in plant genomic studies [ 32 , 33 ]. Besides, due to its extremely high level of gene diversity, maize has high potential in the improvement of yield to meet the demands of population growth [ 33 ]. Despite the combination of economic and genomic impact, the progress in generating a whole genome sequence in maize has been a computational challenge due to the presence of tremendous structural variation (SV) in its genome [ 34 ]. The introduction of NGS techniques in several crops including maize allowed the rapid de novo genome sequencing and production of huge amount genomics and phenomics information [ 1 , 35 ]. A better integration of data within multiple genome assemblies is much needed to study the connection between phenotype and genotype in order to achieve yield and quality improvement of maize [ 35 ]. Nowadays, some user-friendly online databases such as qTeller, MaizeDIG, and MaizeMine are designed to ease the comparison and visualization of relationships between genotypes and phenotypes [ 36 ]. MaizeGDB, a model organism database for maize, provides the access of data on genes, alleles, molecular markers, metabolic pathway information, phenotypic images with description, and more which are useful for maize research [ 35 , 36 ]. MaizeMine is a data mining resource under MaizeGDB, which was designed to accelerate the genomics analysis by allowing the researchers to better script their own research data in downstream analysis [ 36 ] whereas MaizeDIG is a genotype-phenotype database which allows the users to link the association of genotype with phenotype expressed by image [ 35 , 36 ]. Cho et al. [ 35 ] reported that with the accessibility via image search tool, the relationship between a gene and its phenotype features can be visualized within image. The integration and visualization of high-quality data with these tools enables quick prioritizing phenotype of interest in crops, which play a crucial role in the improvement of plant breeding.

Bioinformatics for studying stress resistance in plants

The understanding of the stress response on plants is vital for the improvement of breeding efforts in agriculture, and to predict the fate of natural plants under abiotic change especially in the current era of continuous climate change [ 37 ]. Stress response in plants can be divided into biotic and abiotic. Biotic stress mainly refers to negative influence caused by living organism such as virus, fungi, bacteria, insects, nematodes, and weeds [ 38 ] while abiotic stress refers to factors such as extreme temperature, drought, flood, salinity, and radiation which dramatically affect the crop yield [ 37 ]. NGS technologies and other potent computational tools, which allowed sequencing of whole genome and transcriptome, have led to the extensive studies of plants towards stress response on a molecular basis [ 1 , 2 , 37 ]. The tremendous amount of plant genome data obtained from genome sequencing allows the investigation of correlations between the molecular backbone of living organism and their adaptations towards the environment [ 16 ].

Biotic and abiotic stress management

How the plants and crops respond towards stress environment is the key to ensure their growth and development, and to avoid the great crop yield penalty caused by harsh condition [ 35 , 39 ]. Therefore, the utilization of bioinformatic tools is important to study and analyse the plant transcriptome in response to biotic and abiotic stress. Besides, the application of bioinformatics tools on plants and crops genome can benefit the agricultural community by searching the desired gene among genome from different species and elucidate their function on the crops [ 35 ]. The genome databases play a crucial role in storing and mining large and complex genome sequence from the plants. Besides data storage, some genome databases are also able to perform gene expression profiling to predict the pattern of gene expressed at the level of transcript in cell or tissues. By using in silico genomic technologies, the disease resistance gene-enzyme with their respective transcription factor, which plays a role in defence mechanism against stress, are able to be identified [ 40 , 41 ]. For instance, a large-scale transcriptome sequencing of chrysanthemum plants was carried out by Xu et al. [ 40 ] to study the dehydration stress in chrysanthemum plants. An online database called Chrysanthemum Transcriptome Database ( http://www.icugi.org/chrysanthemum ) was developed to allow the storage and distribution of transcriptome sequence and its analysis result among research community [ 40 ]. With the aid of different protein databases, the biochemical pathway and kinase activity of chrysanthemum in response to dehydration stress are able to be predicted [ 40 ]. Xu et al. [ 40 ] also reported a total of 306 transcription factor and 228 protein kinase that are important upstream regulator in plants when encountered with various biotic and abiotic stresses.

Bioinformatics approaches to study resistance to plant pathogen

One of the challenges in modern agriculture to supply the nutrition’s demand along with the world population growth is the crop loss due to disease. The study of plant pathogen plays an essential role in the study of plant diseases, including pathogen identification, disease aetiology, disease resistance, and economic impact, among others [ 41 ]. Plants protect themselves through a complex defence system against variety of pathogen, including insects, bacteria, fungi, and viruses. Plant-pathogen interaction is a multicomponent system mediated by the detection of pathogen-derived molecules in the form of protein, sugar, and polysaccharide, by pattern recognition receptor (PRRs) within the plants [ 42 , 43 , 44 , 45 ]. After the recognition of enemy molecules, signal transduction is carried out accordingly and plant immune systems will respond defensively through different pathways involving different genes [ 42 ]. According to Schneider et al. [ 46 ], the development of molecular plant pathology can be broadly divided into three eras, begins with the disease physiology starting from early 1900s until 1980s [ 46 ]. In the second era of molecular plant genetic studies, one or a few genes of bacterial pathogens were focused whereas the third era of plant genomic studies began in 2000 with the sequencing of genome, and the first complete genome of bacterial pathogen, Xylella fastidiosa , was obtained [ 46 ]. The recent advance in DNA sequence technologies allow researchers to study the immune system of plants on genomic and transcriptomics level [ 1 , 41 , 42 ]. Genomics has revealed the mystery and complexity and consequently the various information about phytopathogen. A clearer picture of plant-pathogen interactions in the context of transcriptomic and proteomics can be visualized through the application of different bioinformatics tools, which in turn made feasible the engineering resistance to microbial pathogen in plant [ 43 ].

PRGdb: bioinformatics web for plant pathogen resistance gene analysis

Plants have developed a wide range of defence mechanism against different pathogen and ultimately inhibit growth and spread of pathogen [ 47 , 48 ]. Plant defence system is mediated by resistance (R) gene [ 47 ]. R gene plays an important role in defence mechanism. They encode for protein that recognizes specific avirulent (Avr) pathogen proteins and initiated the defence mechanism through one or more signal transduction pathway in a hypersensitive response (HR) [ 41 , 47 , 48 ]. However, the essential components needed for protein to exert their resistance are still unidentified [ 48 ]. With the intention to study and identify more novel R gene, high-throughput genomic experiments and plant genomic sequence are essential to explore their function and new R gene discovery [ 47 ]. In 2009, Plant Disease Resistance Gene database (PRGdb), a comprehensive bioinformatics resource across hundreds of plant species, was launched in order to facilitate the plant genome research on discovery and predict plant disease resistance gene [ 47 , 48 ]. To date, PRGdb 3.0 has been released with 153 reference resistance genes and 177,072 annotated candidate pathogen receptor genes (PRGs) [ 49 ]. This database act as an important reference site and repository to all the research studies on exploration and use of plant resistance genes [ 48 , 49 ].

Apart from resistance gene storage, this easily accessible platform also allows different tools that are essential for exploration and discovery of novel R gene. For instance, the DRAGO 2.0 tool, which was built to explore known and novel disease resistance gene, can be launched on any transcriptome or proteome to annotate and predict PRG from DNA or amino acid with high accuracy [ 49 ]. Besides, BLAST search tools available in PRGdb provide comparison of different sequences which allowed the determination of gene homology and expression analysis. Apart from the database, plant pathology field also benefited from whole genome sequence technologies. The new DNA sequencing technologies such as NGS and Sanger sequencing allowed the study of genomics, proteomics, metabolomics, and transcriptomics on both the host plant and the pathogen [ 1 ]. The phytopathogen genomes which have been sequenced are expected to provide valuable information on the molecular basis for infection of plant host and explore the potential novel virulence factors [ 1 ]. Figure 2 illustrates a brief process involved in producing stress-resistant plant using bioinformatics approach.

Brief process involved in producing stress-resistant plant using bioinformatics approach

Metagenomics in plant biotechnology and Cas9 modification

The effects of environment microorganisms’ community, especially soil microorganism on plants, may contribute to plant’s growth and pathogenesis. Through metagenomics approaches, the soil microorganism community that contributed to plant growth may provide a great genomic insight into physiology and pathology [ 50 , 51 , 52 , 53 ]. In metagenomics approaches, the overall genetic materials obtained from soil are sequenced and advancing to microbial community analysis via data analytics [ 53 , 54 , 55 ]. The extracted genetic materials from the soil were subjected to high-throughput metagenomics analysis via various NGS approaches such as 16S rRNA sequencing, shotgun metagenomic sequencing, MiSeq sequencing [ 54 , 55 , 56 ] for microbial species identification, functional genomics study, and structural metagenomic analysis. A NGS produces huge genomics data for each study; thus, application of bioinformatics tools would add value in the metagenomics analysis as the target genes identified could advance into elucidation of plant growth, plant disease, soil contamination, and microbial taxonomy [ 52 ]. For example, the use of UNITE ( https://unite.ut.ee/ ) for fungi identification [ 57 ], SILVA ( https://www.arb-silva.de/ ) for 16S rRNA [ 58 ], and MGnify ( https://www.ebi.ac.uk/metagenomics/ ) possesses metagenomics data of microbiome [ 59 ]. These databases allow the researchers to retrieve and analyse the relevant metagenomic sequenced data for a specific study.

Since metagenomics analysis provides the greater output on plant-microbe interaction, the genes that are responsible for plant immunity may play a crucial role in protecting against disease-causing microorganism [ 60 , 61 ]. With the emergence of Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) gene editing technique, Cas9 modification could produce a better plant trait and disease-resistant plant [ 62 , 63 ]. The CRISPR/Cas9 system is employed in studying the functional genomics in plants in relation to plant-microbe interaction. CRISPR/Cas9 system facilitated the gene editing by creating a mutant through double-stranded break forming a targeted gene mutation and followed by genome repair [ 63 , 64 , 65 ]. The CRISPR/Cas9 modification on OsSWEET14 genes protects the Super Basmati Rice from bacterial blight causes by Xanthomonas oryzae pv. oryzae [ 66 ]. Gene editing to knockout OsMPK5 and OsERF922 genes in rice protects against Magnaporthe grisea and Magnaporthe oryzae , respectively [ 67 , 68 , 69 ]. Besides that, Cas9 modification on Cs WRKY22 and TcNPR3 increased host defence immunity through regulating salicylic acid in Citrus sinensis and Theobroma cacao , respectively [ 70 , 71 ]. Thus, CRISPR/Cas9 modification could be one of important science advancements to validate the metagenomics analysis on plant-microbe interaction.

Current challenges of bioinformatics applications in plant biotechnology

Despite the beneficial prospect of the bioinformatics applied in plant biotechnology, there are many challenges and limitations must be addressed in order to fully utilize their potentials [ 1 ]. Along with the rapid growth in plant genome data mining and database development, there are a few challenges faced by bioinformaticians and scientists which can be divided into number of areas as mentioned in the subsections below.

Bioinformatic data management and organization and synchronize update resources

Since the introduction of the next-generation sequencing (NGS), which is commercially available in 2004, enormous amount of data has been generated in plant genome research. Thousands of Gb of plants sequences are deposited in various public databases monthly [ 1 , 72 , 73 ]. Moreover, the constantly sequenced and re-sequenced of the plant genome has developed a vast amount of new genome sequence in all public databases. The increase in sequenced plant genome driven by technological improvement has led to a problem that arises along with the storage and update of a large amount of data [ 72 , 74 ]. The update process should occur in all the comparative databases, not just solely individual genome database [ 72 ]. With this, the synchronized update of genome data resources among different plant genomic platform is able to provide a strong, updated, reliable database community that all the plant researchers can rely on [ 72 ].

Complexity of plant genetic content

Other than the tremendous amount of genome sequence generated, the complexity of the plant genetic content is also a challenging issue faced by plant research community. Even though the arrival of next-generation sequencing technologies has allowed the rapid DNA sequencing for non-model or orphan plant species, the sequencing pace for plants is far from that of animal and microorganism [ 74 ]. The main factor which contributes to this situation is because sometimes the plant genome can be nearly hundred times larger than the currently sequenced animal and microorganism genome [ 73 ]. Needless to say, some of the plant genome even can have polyploidy, a duplication of an entire genome, which is estimated to occur in 80% of the plant species [ 73 , 75 ]. According to Schatz et al., the genome assembly in the case of large size plant genome with abundance of repetitive sequence can be metaphorically described as build-up of a large puzzle consisting of blue sky separated by nearly indistinguishable white clouds of small gene [ 73 ]. The particular reason for this is mainly because the sequence length in NGS is relatively shorter than in Sanger sequencing and required dedicated assembly algorithm [ 74 ]. Therefore, most plant genomes sequenced by NGS can only be used for establishing gene catalogues, interpreting the repeat content, glimpsing evolutionary mechanism, and performing on comparative genomics in early study [ 74 ].

Advance in sequencing technologies

There are two basic approaches to genome assembly, i.e. comparative genome assembly and de novo genome assembly [ 75 ]. It is important to distinguish between these two different approaches. Comparative is a reference-guided method which use a genome or transcriptome, or both, for guidance, whereas de novo assembly refers to reconstruction of a genome from organisms that have not been sequenced before [ 74 , 75 ]. Table 2 compares some of the available assembly and NGS technology available for genome sequencing. However, these two approaches are not completely exclusive due to a lack of bioinformatic tools designed to cope with the unique and challenging features of plant genomes [ 74 , 75 ]. One of the biggest challenges in the development of bioinformatic software is the algorithm development [ 76 ]. As is known, all the programmes or software in bioinformatic are very computationally intensive. As most of the assemblies available now solely rely on single assembly, a development in better algorithm in terms of resource requirement is essential for combining different assemblers by using a different underlying algorithm in order to give a more credible final assembly [ 74 , 76 ].

Database accessibility

To date, there are about 374,000 known plant species in the world [ 77 ]. The first full plant genome sequencing was completed on A rabidopsis thaliana through Sanger sequencing methods in 2000 [ 78 ]. Although introduction of molecular biology decades ago may have facilitated the species identification, obtaining the full plant genomic data remains challenging due to the genome complexity. The development of NGS platform may foster the plant genome sequencing, yet there are limited sequenced datasets reposited to the database. To date, there are only 29 plant genome databases accessible in PlantGDB genome browser allowing researchers to retrieve the information about gene structure, matched GSS contigs, similar protein, spliced alignments EST, etc. Besides, the PlaD database ( http://systbio.cau.edu.cn/plad/index.php ) that focuses on the microarray data of the plants developed by China Agricultural University comprises transcriptomic database for plant defence against pathogen. However, it is limited to Arabidopsis , rice, maize, and wheat [ 79 ]. The Plant Omics Data Center ( http://plantomics.mind.meiji.ac.jp/podc/ ) is another publicly available web-based plant database featuring omics data for co-expressed profile, regulatory network, and plant ontology information [ 80 ]. Although curated omics datasets could be retrieved from PODC, information are restricted for certain plants and crops such as Arabidopsis , tobacco, earthmoss, barrelclover, soybean, potato, rice, tomato, grape, maize, and sorghum. Furthermore, all these publicly available databases require constant updating with new released data or resequencing data so that the researcher could obtain the most updated version of genome datasets for their research.

The application of bioinformatics in plant biotechnology represents a fundamental shift in the way scientists study living organisms. Bioinformatics play a significant role in the development of agriculture sector as it helps to study the stress resistance and plant pathogen, which are critical in advancing crop breeding [ 75 ]. NGS and other sequencing technologies will make more plant genome data accessible in all public databases and enable the identification of genomic variants and prediction of protein structure and function [ 75 , 76 ]. Moreover, GWAS, which allows the identification of loci and allelic variation related to valuable traits, eased the crop modification and improvement [ 74 ]. In brief, the advance in bioinformatics application in plant biotechnology enables researchers to achieve fundamental and systematic understanding of economically important plant. However, despite all these exciting achievement by the application of bioinformatic on plant biotechnology, it is still a long way from automated full genome sequencing and assembly at a low cost [ 76 ]. There is a critical need for effective bioinformatic tools which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant’s genome. To achieve this, an enhanced algorithm development is essential to enable data mining and analysis, comparison, and so on. Therefore, bioinformaticians and experts with mathematical and programming skills will play an important role in bringing fresh approaches and knowledge into bioinformatics, not only for the advancement in plant biotechnology and agriculture sector, but the future of humanity as well.

Availability of data and materials

Not applicable.

Abbreviations

Genome-wide association studies

Next-generation sequencing

Plant Disease Resistance Gene database

RNA sequencing

Single-nucleotide polymorphism

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Tan, Y.C., Kumar, A.U., Wong, Y.P. et al. Bioinformatics approaches and applications in plant biotechnology. J Genet Eng Biotechnol 20 , 106 (2022). https://doi.org/10.1186/s43141-022-00394-5

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The lack of innovative standards for biosafety in synthetic biology is an unresolved policy gap that limits many potential applications in synthetic biology. We argue that a massive support for standardization in biosafety is required for synthetic biology to flourish.

• Michele Garfinkel
• Markus Schmidt

Constructive principles for gene editing oversight

• L. Val Giddings
• Richard J. Roberts

Responsible governance of gene editing in agriculture and the environment

• Doria R. Gordon
• Gregory Jaffe
• Melissa D. Ho

CO 2 fixation gets a second chance

Synthetic metabolic pathways that circumvent photorespiration can improve crop growth. Now, an efficient photorespiration bypass with a new-to-nature carboxylation step has been engineered and demonstrated in vitro.

• Markus Janasch
• Elton P. Hudson

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GRADUATE APTITUDE TEST IN ENGINEERING 2025

अभियांत्रिकी स्नातक अभिक्षमता परीक्षा २०२५, organising institute: indian institute of technology roorkee.

GATE 2025 TEST PAPERS & SYLLABUS

GATE 2025 will be conducted for 30 test papers. The following table shows the list of papers with codes. Please click the Paper/Code to download the syllabus.

A candidate is allowed to appear either in ONE or UP TO TWO test papers. Please see the page Two-Paper Combination for more details.

The test papers will be in English. Each GATE 2025 paper is for a total of 100 marks, General Aptitude (GA) is common for all papers (15 marks), and the rest of the paper covers the respective test paper syllabus (85 marks). Click here for detailed pattern of the question papers .

Multi-sessional papers: Candidate will be assigned to appear only in one of the sessions for the papers running in multiple sessions.

Computer Science and Information Technology (CS) and Civil Engineering (CE) will be conducted as multi-session papers in GATE 2025. More precisely, they will be two-session papers. This means that the candidates will be assigned to one of the sessions only — either the forenoon session or the afternoon session. The question papers will be different for each session. Test papers are held in multiple sessions when the candidate count is so high that they cannot all appear for the test in the same session. The scores of the candidates will be normalized according to the normalization formula given in Section 13.2 of the Information Brochure.

Candidates must familiarize themselves with the paper code as it is required both during application and examination.

Each candidate should fill ONLY ONE application. If they wish to appear in second paper (from the two-paper combination), they can add respective paper in their original application. In case of Multiple applications, only one will be accepted and remaining applications will be rejected without any refund for the paid fee.

IISc Bengaluru

IIT Guwahati

IIT Kharagpur

IIT Roorkee