Molecular Biotechnology Glick Free Pdf Download

... Molecular method in order to study the epidemiology of food-borne diseases is usually using DNA subtyping. Genomic DNA profiles in DNA subtyping are divided according to the size, and the resulting size will form the patterns which can be used as a characterization of each isolate [19] . Some DNA subtyping methods are commonly used for the characterization of bacterial genomes including pulsed-field gel electrophoresis, ribotyping, and random amplified polymorphic DNA (RAPD) [20,21]. ...

... Pulsed-field gel electrophoresis subtyping as one of the fingerprinting methods usually use restriction enzymes that cut genomic DNA randomly to generate approximately 20-30 fragments. The size of the fragments formed quite varied between 10 and 1 000 kbp and this method requires a separation method with special electrophoresis [19,20] . On the other hand, ribotyping method also uses restriction enzymes. ...

... Glick and Pasternak revealed that the primer or short oligonucleotides used in genomic analysis would form pairs in many places with chromosomal DNA. The number of amplified DNA fragments would depend on the primers used, and the result could be used to determine the characteristic of the entire genome or the chromosome of an individual [19]. Accuracy of AP-PCR as one of the fingerprinting methods with a great sensitivity and efficiency had proved by researcher [40]. ...

Objective: To evaluate the zoonotic potency of Escherichia coli O157:H7 through arbitrarily primed-PCR (AP-PCR) methods as one of the DNA fingerprinting methods. Methods: A total of 14 isolates consisted of 11 isolates originated from human feces with renal failure symptoms, 2 isolates originated from cattle feces, and 1 control isolate were used in this study. DNA of each isolate was extracted, and their profiles were studied by using AP-PCR method with M13 F and M13 R arbitrary primers. Results: The results founded that all of 14 isolates had similarity range from 54.6% to 88.5%. Isolates KL-106(3) and KL-55(6) originated from humans showed the degree of similarity with isolates SM-25(1) and SM-7(1) originated from cattle as high as 85% and 77%, respectively. Conclusions: The high degree of similarity between isolates originated from cattle and human indicated the high potency of zoonoses. The results also concluded AP-PCR method as a briefly fingerprinting method in order to trace the epidemiological of E. coli O157:H7

... Since cpDNA paternal contribution in angiosperms has not been reported extensively, and mitochondria are crucial during pollen tube germination (Twell et al., 2006), we assume that P. volubilis cpDNA is maternally inherited and its mtDNA is biparentally inherited. However, it is necessary to experimentally determine the cpDNA inheritance mode in P. volubilis, which is essential information for enabling successful genetic improvement programs, avoiding unwanted crosses with wild germplasm (Glick and Patten, 2017). It would appear suitable to develop genetically modified cultivars, harboring cpDNA modifications, avoiding gene scape. ...

... It would appear suitable to develop genetically modified cultivars, harboring cpDNA modifications, avoiding gene scape. In cpDNA enhanced plants, higher expression of proteins is manifested, allowing them to overcome biotic and abiotic stress (Glick and Patten, 2017). In order to determine the cpDNA mode of transmission, psbA-trnH GUG IS was used as a chloroplast sequence marker in crossbreeding experiments of the present study's cultivars. ...

... In order to determine the cpDNA mode of transmission, psbA-trnH GUG IS was used as a chloroplast sequence marker in crossbreeding experiments of the present study's cultivars. Therefore, solving cpDNA inheritance mode in P. volubilis is a stepping stone to decide how to develop modified cultivars eventually that could avoid unwanted crosses with wild germplasm (Glick and Patten, 2017). ...

Plukenetia volubilis L. (Malpighiales: Euphorbiaceae), also known as Sacha inchi, is considered a promising crop due to its high seed content of unsaturated fatty acids (UFAs), all of them highly valuable for food and cosmetic industries, but the genetic basis of oil biosynthesis of this non-model plant is still insufficient. Here, we sequenced the total DNA of Sacha inchi by using Illumina and Nanopore technologies and approached a de novo reconstruction of the whole nucleotide sequence and the organization of its 164,111 bp length of the chloroplast genome, displaying two copies of an inverted repeat sequence [inverted repeat A (IRA) and inverted repeat B (IRB)] of 28,209 bp, each one separating a small single copy (SSC) region of 17,860 bp and a large single copy (LSC) region of 89,833 bp. We detected two large inversions on the chloroplast genome that were not presented in the previously reported sequence and studied a promising cpDNA marker, useful in phylogenetic approaches. This chloroplast DNA (cpDNA) marker was used on a set of five distinct Colombian cultivars of P. volubilis from different geographical locations to reveal their phylogenetic relationships. Thus, we evaluated if it has enough resolution to genotype cultivars, intending to crossbreed parents and following marker's trace down to the F1 generation. We finally elucidated, by using molecular and cytological methods on cut flower buds, that the inheritance mode of P. volubilis cpDNA is maternally transmitted and proposed that it occurs as long as it is physically excluded during pollen development. This de novo chloroplast genome will provide a valuable resource for studying this promising crop, allowing the determination of the organellar inheritance mechanism of some critical phenotypic traits and enabling the use of genetic engineering in breeding programs to develop new varieties.

... On one hand, PCR inefficiency is correlated with low amounts of DNA recovered from hemalum-stained FFPE tissues (Serth et al. 2000). PCR is a very sensitive technique and as in each cycle the DNA content is doubled, the initial amount of DNA template is usually not an issue (Glick et al. 2010). However, the whole amount of DNA recovered from microdissected FFPE histological sections is usually very low, which might constitute a limiting factor for PCR (Glick et al. 2010). ...

... PCR is a very sensitive technique and as in each cycle the DNA content is doubled, the initial amount of DNA template is usually not an issue (Glick et al. 2010). However, the whole amount of DNA recovered from microdissected FFPE histological sections is usually very low, which might constitute a limiting factor for PCR (Glick et al. 2010). Furthermore, it has been observed that hemalum itself seems to be inhibitory to PCR, as destaining restores DNA amplificability (Chen et al. 1996). ...

... Accordingly, another possible mechanism by which hematein inhibits PCR is through the binding and consequent rescue of the available divalent cations from the reaction. The replication ability of Taq DNA polymerase is highly dependent on the presence of divalent cations (normally magnesium), and its absence or excess determines the success of PCR (Glick et al. 2010). Indeed, it has been demonstrated that concentrated H&E-stained sample results in unfaithful CGH profiles (Hirose et al. 2001;Huang et al. 2005) in opposition to dilute samples and that increasing the magnesium concentration during DOP-PCR improves the CGH results (Hirose et al. 2001). ...

Alexandra Pote
Otilia Boghenco
Ana Marques-Ramos

Molecular pathology allows the identification of causative agents in infectious diseases and detection of biomarkers important for prediction of disease susceptibility, diagnosis and personalized therapy. Accordingly, nucleic acid-based methods have gained a special role in clinical laboratories particularly to evaluate solid and hematological tumors. Extraction of nucleic acids is commonly performed in microdissected formalin-fixed paraffin-embedded (FFPE) or cytological samples that had been previously evaluated through the use of hematoxylin and eosin (H&E) or Papanicolau (Pap) stains, respectively. Although the effect of both stains on nucleic acids integrity has been explored by several authors, the results are not consistent and require further examination. Accordingly, the goal of this review was to assess the influence of H&E and Pap stains on DNA and RNA integrity and to address the mechanism by which each staining compromises molecular based-analysis. The analyzed studies demonstrate that H&E- and Pap-staining result in low DNA recovery and some degree of DNA fragmentation. Additionally, it is concluded that hemalum inhibits PCR by interfering with DNA extraction, preventing DNA polymerase attachment and possibly by rescuing divalent cations. Accordingly, proper sample purification and adjustment of PCR conditions are of key importance to achieve satisfactory results by PCR in H&E- and Pap-stained samples. Furthermore, although H&E results in RNA fragmentation, it is possible to perform expression analysis in H&E-stained frozen sections, using RNase-free conditions, low amounts of hematoxylin and a rapid protocol from sample collection to RNA analysis. It The effect of Pap-staining on RNA integrity remains to be determined.

... Gen düzenleme teknolojilerinin temelini oluşturan rekombinant DNA teknolojisi genetik bilginin (DNA) bir organizmadan diğerine aktarılmasına dair bir dizi deney protokolünü kapsar. Bu teknolojinin gelişimi, daha çok bakteriyofaj ve plazmitlerin genetiği üzerine yapılan çalışmalarla olmuştur (4). 1970 yılında retrovirüslerin kendi RNA'larından DNA kopyalamak için ters transkriptaz enzimini kullandıkları keşfedilmiş, ardından 1972' de Paul Berg, viral bir genom içine yabancı bir dizini sokarak bir maymun virüsünün (SV40-Simian virus 40) DNA'sını lambda fajının DNA'sı ile birleştirmeyi başarmış, böylece ilk rekombinant DNA molekülleri oluşturulmuştur (5). ...

... Öyle ki YND kullanılarak bütün bir insan genomunun tek bir gün içinde dizilenebilmesi mümkün hale gelmiştir. Farklı özelliklerdeki gen parçacıkları kolayca birleştirilebilmekte, farklı hücrelere aktarılabilmekte, sadece mikroorganizmalar değil, aynı zamanda bitkiler ve hayvanlar da genetik olarak tasarlanabilmektedir (8,4). Bu teknik gelişmeler sonucunda, gen düzenleme teknolojileri çok geniş bir kullanım alanı (kanser, gen terapisi, hormon üretimi, aşı yapımı gibi tıbbi alanlardan tarım ve hayvancılığa ve hatta biyoteknolojik pil üretimine kadar) bulmaktadır (9). ...

... More than 12 000 antibiotics with a variety of modes of action and with different specificities have been extracted from different microorganisms, since the late 1920s when penicillin was first discovered [46,47]. The first use of the term "antibiotic" in the present sense was by the American microbiologist Waksman and his colleagues in 1941 [48]. ...

... In the antibiotic market, the sales are driven by four leading drug classes: the cephalosporins (27%), macrolides (20%), quinolones (17%), and penicillins (17%). These four drug classes, together, account for more than 80% of the global antibacterial sales [46]. ...

... Once again, however, it was the pursuit of human health-related knowledge that motivated the innovation needed to make environmental inquiry feasible: sequencing the human genome. The first human genome was completed in 2003 using whole-genome shotgun sequencing at a cost of $2.7 billion dollars over 15 years (Bernard et al. 2010;Lander et al. 2001). The Human Genome Project and the parallel efforts in yeast and worms laid out the strategy to deal with large-scale genomic sequencing. ...

Bioremediation is generally viewed as a cost-effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next-generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from its roots in biology and medicine to its current status in environmental engineering, including potential future directions in commercial application.

... Molecular cloning generally uses DNA sequences from two different organisms, the species that is the source of the DNA to be cloned, and the species that will serve as the living host for replication of the recombinant DNA. Molecular cloning methods are central to many contemporary areas of modern biology and medicine (Cheryl et al., 2009). Cloning involves the construction of hybrid DNA molecules that are able to self-replicate in a host cell, usually bacteria. ...

... Molecular biotechnology allows researchers to transfer particular units of genetic information between organisms to improve their values [1]. Gene is expressed as a response to accumulated specific signal and this system is used by the researchers to control which chemicals or materials are produced by the cells. ...

Rahmat Azhari Kemal
Annisa Novianti
Ilma F Ma 'ruf
Ruli Fatmawati

Cellular systems can be engineered by synthetic biology approach to make a controllable bioremediation system.Several teams competing in the International Genetically Engineered Machine (iGEM) competition have utilized the potency of synthetic biology for bioremediation. This review highlighted several ideas. One of them is the designing a whole-cell biocatalyst that can degrade PET component in plastic waste. Rice blast (Magnaporthe grisea) produces cutinase, thus its gene encoding cutinase can be used as substitute in the system. Regulation of the application is also discussed. It is hoped that research and implementation of bioremediation using synthetic biology in Indonesia can be developed.

... A la différence des plantes génétiquement modifiées, ce saumon transgénique fait l'objet de vives controverses, en particulier dans les Etats américains ayant une importante activité de pêche de poissons sauvages. L'ensemble des techniques mises en oeuvre pour les OGM évolue rapidement avec le recours à des systèmes plus précis de transformation du noyau, la transformation des plastides, l'utilisation des systèmes de « silencing », pour ne pas parler de la biologie synthétique (COHAN, 2010 ;FRIZZI and HUANG, 2010 ;GLICK et al., 2010 ;LUSSER et al., 2011 ;WEATHERS et al., 2010). Après une première commercialisation en 1994 d'une tomate à maturation retardée, les premières cultures commerciales de soja tolérant à un herbicide commencèrent aux USA et les premiers OGM arrivèrent dans les ports européens en 1996. ...

Yves Bertheau

Genetically modified organisms (GMO) constitute one of the most important innovations in agricultural production over the 2 last decades. While GMO cultivation is highly developed in some third countries, it is rather small in the European Union. Reluctance of some consumers and producers led the European Union to settle this complex legislative framework by conserving the freedom of choice of consumers through labelling and supply chain coexistence and of producers through production coexistence. Plant biology, territory organization by supply chains downstream operators, societal aspects and economics make the definition and implementation of coexistence rules very complex. The practical lower threshold, used by supply chains' operators, and the GMO-free low threshold all militate for a coexistence mode based on collectively organized dedicated production areas instead of flexible coexistence based on the choices of individual farmers. This paper provides a summary of elements for further thinking on these two coexistence frames.

... Like other molecular markers, RAPDs can be used to characterize whole genomes, individual chromosomes, or, less commonly, specific genes. Although the procedure was originally developed for plants, it is also useful in the characterization of microorganisms (Glick, Bernard J. 2010). ...

Syed Raju Ali

Assignment on Random Amplified Polymorphic DNA (RAPD)

... Cloning of genes controlling expression of agronomical traits can considerably advance molecular breeding (Glick et al. 2010). For example, genes of traits under simple genetic control, as resistance to some diseases and pests (Gusberti et al. 2013), control of ripening (Barry et al. 2006), or tree architecture (Dardick et al. 2013) can be transferred to, or specifically blocked in selected genomes, triggering expression of the desired traits in superior cultivars. ...

Igor V Bartish

Sea buckthorn (Hippophae L., Elaeagnaceae) has been exploited by humans for thousands of years on the Quinghai–Tibetan Plateau (QTP) and nearby areas. However, the considerable modern economic potential of this plant has started to receive full appreciation only recently. Expanding its traditional use in harsh climatic zones as important source of nutrients, vitamins, and as wood in treeless areas, today this plant is used also on large scales as landscape protection tools against corrosion of soil, and as a source of wide range of products in pharmaceutic, cosmetic, and nutritional supplement industries. This review aims to provide the latest insights from studies on the evolutionary history and biogeography of the genus, structure, and phylogeography of genetic diversity within its species. Understanding the genic and genomic interactions among populations and phylogenetically distant lineages within species of Hippophae should help to improve the efficiency of exploitation of genetic resources in this crop. Research efforts in the past century in breeding, systematics, cytogenetics, biochemistry, and genetics of Hippophae have created a solid background for advances in modern biotechnology of this crop. Recent studies reported application of next-generation sequencing (NGS) technologies and identification of thousands of genes in transcriptomes of sea buckthorn. Analyses of the transcriptomes provided better understanding of gene expression in biochemical pathways of unsaturated fatty acids, some other secondary metabolites, and regulation of gene complexes responsible for adaptation to different categories of abiotic stress. Further studies should focus on the creation of genetic maps of breeding populations; identification of quantitative trait loci, biochemical pathways of synthesis of bioactive secondary metabolites and correspondent genes, molecular mechanisms of tolerance and resistance to abiotic stress, diseases, and pests; and cloning of genes of agricultural importance. Advances in these research areas can lead to genetic engineering of plants with a combination of traits of high horticultural, medicinal, or nutrient value, adapted to specific environments of areas of their cultivation.

... Similarly, they are the most predominant group of microbes that degrade xenobiotic compounds. It is well documented that various bacteria from genus Pseudomonas, including P. aeruginosa strains, inhabit hydrocarbon-contaminated soils and can break a wide range of different organic compounds (Glick et al. 1994;Hong et al. 2005;Saikia et al. 2012;Pacwa-Płociniczak et al. 2014). They are the well-known bacteria that have the capability of utilizing a number of aliphatic and aromatic hydrocarbon compounds as a carbon and energy sources (Das and Chandran 2010;Kadali et al. 2012;Puškárová et al. 2013). ...

Among 348 microbial strains isolated from petroleum hydrocarbon-contaminated soil, five were selected for their ability to produce biosurfactant based on battery of screening assay including hemolytic activity, surface tension reduction, drop collapse assay, emulsification activity, and cell surface hydrophobicity studies. Of these, bacterial isolate DSVP20 was identified as Pseudomonas aeruginosa (NCBI GenBank accession no. GQ865644) based on biochemical characterization and the 16S rDNA analysis, and it was found to be a potential candidate for biosurfactant production. Maximum biosurfactant production recorded by P. aeruginosa DSVP20 was 6.7 g/l after 72 h at 150 rpm and at a temperature of 30 °C. Chromatographic analysis and high-performance liquid chromatography-mass spectrometry (HPLC-MS) revealed that it was a glycolipid in nature which was further confirmed by nuclear magnetic resonance (NMR) spectroscopy. Bioremediation studies using purified biosurfactant showed that P. aeruginosa DSVP20 has the ability to degrade eicosane (97 %), pristane (75 %), and fluoranthene (47 %) when studied at different time intervals for a total of 7 days. The results of this study showed that the P. aeruginosa DSVP20 and/or biosurfactant produced by this isolate have the potential role in bioremediation of petroleum hydrocarbon-contaminated soil.

... A la différence des plantes génétiquement modifiées, ce saumon transgénique fait l'objet de vives controverses, en particulier dans les Etats américains ayant une importante activité de pêche de poissons sauvages. L'ensemble des techniques mises en oeuvre pour les OGM évolue rapidement avec le recours à des systèmes plus précis de transformation du noyau, la transformation des plastides, l'utilisation des systèmes de « silencing », pour ne pas parler de la biologie synthétique (COHAN, 2010 ;FRIZZI and HUANG, 2010 ;GLICK et al., 2010 ;LUSSER et al., 2011 ;WEATHERS et al., 2010 du JRC IHCP avec l'appui du réseau ENGL) • à participer financièrement aux frais occasionnés. Si ces obligations constituent un net progrès pour les laboratoires de contrôle, il faut pourtant souligner que l'EURL-GMFF ne dispose pas d'un mandat suffisant, ni pour valider des méthodes de criblage utiles en détection d'OGM non autorisés, ni pour revalider des méthodes fournies par les pétitionnaires qui s'avéreraient insuffisantes. ...

E. Glon

The European Union scenarios to promote the coexistence of GM crops and conventional or organic crops imply segregated spatial planning, an agricultural approach of the rural space and geographical areas as continuous and homogenous elements. All of these points are disputable for a geographer. So, this study aims to consider a geographical analysis of this coexistence and also how territorial populations and councils can express their opinion on this subject.

... [57] Proteomics It aims to characterize all proteins in a biological sample at the functional level. [58] Metabolomics It is used to describe the quantitative analysis of all metabolites in a biological system such as cell, tissue, or biological fluid. [59] Nutrigenomics It aims to reveal the relationship between nutrition and the genome and to provide the scientific basis for improved public health through dietary means. ...

In dentistry we encounter numerous differences in the dentofacial characteristics of individuals, even among family members. The three most common problems in dentistry today remain dental caries, periodontal diseases and malocclusion. A multifactorial aetiology for all three conditions has generally been assumed, with both genetic and environmental contributions to observe variability .This article describes the some of the dental disorders and its genetic etiology.

... Traditional Cloning is the cloning in which we use restriction endonucleases to produce DNA fragments with specific complementary end sequences that can be joined together with a DNA ligase enzyme, prior to the transformation [2]. This technique involves preparing both a DNA fragment which is going to be cloned (insert) and a DNA plasmid (vector) in which we are going to ligate our gene of interest, by cutting with two unique restriction enzymes that flank the DNA sequence on both sides with sticky ends, and whose cut sites are present at the preferred site of insertion of the vector, called the multiple cloning site (MCS) [3]. By using two different REs, two non-compatible ends are generated in the vector which were not ligated to itself, thus forcing the insert to be cloned directionally, and lowering the transformation background of re-ligated vector alone so this method is accurate at some extent. ...

Yves Bertheau

... The phylogenetic analysis of P-1 revealed that close relatives of this strain are strains belonging to P. aeruginosa. It has been reported that various bacteria from genus Pseudomonas, including P. aeruginosa strains, inhabit oil-contaminated soils and can break down more than 100 different organic compounds (Glick et al. 1994; Hong et al. 2005; Saikia et al. 2012). They are the best known bacteria capable of utilizing a number of aliphatic and aromatic hydrocarbons as carbon and energy sources (Das and Chandran 2011; Kadali et al. 2012; Puškárová et al. 2013). ...

The Pseudomonas sp. P-1 strain, isolated from heavily petroleum hydrocarbon-contaminated soil, was investigated for its capability to degrade hydrocarbons and produce a biosurfactant. The strain degraded crude oil, fractions A5 and P3 of crude oil, and hexadecane (27, 39, 27 and 13 % of hydrocarbons added to culture medium were degraded, respectively) but had no ability to degrade phenanthrene. Additionally, the presence of gene-encoding enzymes responsible for the degradation of alkanes and naphthalene in the genome of the P-1 strain was reported. Positive results of blood agar and methylene blue agar tests, as well as the presence of gene rhl, involved in the biosynthesis of rhamnolipid, confirmed the ability of P-1 for synthesis of glycolipid biosurfactant. (1)H and (13)C nuclear magnetic resonance, Fourier transform infrared spectrum and mass spectrum analyses indicated that the extracted biosurfactant was affiliated with rhamnolipid. The results of this study indicate that the P-1 and/or biosurfactant produced by this strain have the potential to be used in bioremediation of hydrocarbon-contaminated soils.

... Development of various industries, farming and growth rate of population in the world, have caused the distribution of different types of pollutions into environment. As an example, the worldwide production in 1985 of just one chemical that is released into the environment pentachlorophenol was more than 50,000 tons [33]. In this way, a large scale screening method is necessary to detect and remove the pollution compounds. ...

... However, until now, GMO producers have not released GMOs with improved organoleptic or nutritional improvements, nor industrial products such as pharmaceuticals which appear to be more acceptable to consumers. In parallel, several new genetic modification tools, epigenetic based tools and synthetic biology have appeared over the last few years which allow cleaner transformation of plants with, for instance, directed mutagenesis of specific loci, or provide a completely new organism (Cohan, 2010; Frizzi and Huang, 2010; Glick et al., 2010; Lusser et al., 2011; Mirouze and Paszkowski, 2011). The status of these new modified organisms (i.e. ...

This chapter describes the European framework which induced coexistence and traceability needs in the EU. After having rapidly reviewed the context of GMO development, production and trade, this chapter outlines the socio-economic issues and consumers' concerns raised by the introduction of GM plants into the agricultural system. It then summarizes increasing demands of consumers for safe and healthy produce, generally represented by "quality signs". After summarizing the European regulatory framework, it develops the actions undertaken by the European Commission and EU member states for satisfying the often conflicting, freedom of cultivation of the farmers and freedom of choice for European consumers. The 2 main results are the coexistence of supply chains' with an important traceability framework. The actions encompass, in particular, an enforcement network for traceability, with the duties for companies to provide detection methods of GMOs and to financially participate to the incurred costs of methods validation, research projects on traceability and coexistence issues. Some coexistence rules in place were either enacted by EU –MS, developed by the farmers and their organizations, or both. Finally, the commercialization of GMOs shall be accompanied in the EU by the post-market monitoring of environment and human health whose implementation is far from easy. This European frame of coexistence and traceability targets a peaceful development of GMO despite a very controversial situation, and should ensure that next generations of GMO, designed for e.g. pharmacy and industry, will not enter the food and feed chains.

... [32] Recombinant DNA technology This can be used in variable number tandem repeated in forensic medicine, this technology is helpful for gene therapy production of transgenic animals and plants and also recombinant drugs. [33] Transcriptome analysis The term used to describe the approach in which mRNA, and consequently gene expression, is analyzed in a biological sample under certain conditions at a given point in time. [34] Proteomics It aims to characterize all proteins in a biological sample at the functional level. ...

Rashmi Rai
P.G.Naveen Kumar
SushanthV Hirekalmath
LA Sunil

There is a lack of knowledge regarding genetic diseases and its prevention among general population an important premise is that a better understanding of the genetic etiology of the diseases can facilitate early detection in high risk subjects. It also helps in designing more effective intervention strategies. Exciting new technology based on the foundation of genetic research has the potential to further enhance the quality of life. Progress in the field will require training of a new generation of the scientists with requisite skills, as well as greater collaboration and interdisciplinary work. The traditional epidemiologic approach has proved useful for generating hypotheses and unraveling disease etiologies. But now it is possible to go beyond these methods and look inside the black box of the disease process which would be able to change the definition of the risk factors or clarify their location in the casual model.

Iskandar Z Siregar

Attempt to rehabilitate degraded natural forests in Indonesia is recently carried out by applying selective cutting and line planting (TPTJ) silvicultural system. One of the most important aspects of TPTJ silvicultural system is the procurement methods of large number of planting stocks. Shorea johorensis Foxw was investigated in this regards as one of promising Shorea species for rehabilitating degraded forests due to its fast growing character. The species is usually propagated by three different propagation techniques, namely up-rooted seedlings, seeds and cuttings. Genetic consequences due to different propagation methods in this species are poorly known and need to be studied in order to determine genetic variation and differentiation. Material from five origins (populations), namely: (i) up-rooted seedlings, (ii) seeds, (iii) cuttings, (iv) young plantation and (v) natural forest were randomly taken in the field and subsequently assessed by RAPD using threepreviously tested random primers of OPO-11, OPO-13 and OPO-16. Results showed that natural tree populations showed the highest levels of genetic variation with mean values na = 1.2593, ne = 1.2070, PLP = 25.93% and He = 0.1109. Cutting populations showed the lowest levels of genetic variation with mean values na = 1.1111, ne = 1.0773, PLP = 11.11% and He = 0.0445. Meanwhile, according to the propagation techniques, up-rooted seedling population revealed the highest levels of genetic variation with mean values na = 1.2222, ne =1.1613, PLP = 22.22% and He = 0.0886. Particular methods of plant propagation in this company, especially cutting method, reduced significant genetic variation of S. johorensis.Key words: Shorea johorensis Foxw, RAPD, genetic variation, silvicultural system

Ramesh Chandra

In the present study, the gene of invertase enzyme from Bacillus megaterium was cloned and expressed in non-invertase producing E. coli. Bacillus megaterium was isolated from soil and identified by performing various biochemical tests. Then the isolation of genomic DNA followed by electrophoresis on a 0.8% agarose gel was done. Amplification of gene of interest using invertase primer was done by PCR. The amplified product observed in 1.2% gel stained with ethidium bromide. This PCR product was further subjected to restriction digestion (EcoRI) and then ligation with the vector (Plasmid DNA pUC18). A competent cell of the target bacteria (invertase non-producing) was prepared using chemical method (CaCl2). The ligation mixture was allowed to react with the competent cells in order to uptake the DNA insert ligated with the vector. The mixture was spread over the nutrient agar plates added with the antibiotics (Ampicillin). The transformed E. coli cells were screened by observing the presence of colonies over the nutrient agar plate as the transformed cells showed the property of antibiotic resistance.

Prakash S Bisen

This 1,700-plus page book is true to its title―it is a comprehensive book of laboratory protocols used in all applied life sciences. … The purpose is to provide an integrated laboratory protocols book, 'arranged and presented in a way comprehensible' to students of interdisciplinary fields (e.g., life sciences, biotechnology, etc.). The book meets these worthy objectives. … While the book is intended for undergraduate or graduate students in interdisciplinary life sciences, it would be useful to a much wider audience―extending to junior and high school science teachers, as well as postgraduate (including practicing) practitioners in all life sciences fields. … Wow―this book is unbelievable. For those of you who remember encyclopedias, this is the encyclopedia of laboratory protocols. It isoverwhelming in the sheer breadth of the material it covers. ... Each section has a concise description of the technology, followed by a list of suggested readings and useful links. I started with the microscopy chapter. It was one of the most succinct, concise, and clear discussions I've ever encountered. The illustrations are self-explanatory. I feel confident I can now perform Kohler illumination successfully. … Many of these protocols are being taught today in junior high and high schools, so this would be a great reference for these science teachers. The chapters and protocols covering conventional clinical laboratory protocols (bacteriology, virology, hematology, blood banking, etc.) are too simplistic for the typical clinical laboratory, but would serve as excellent introductory educational materials. Finally, the color inserts are simply fabulous. … If you really want a single book containing pretty much all of the laboratory protocols for every aspect of the life sciences, get this one. … Weighted numerical score: 91 - 4 stars." ―Valerie L. Ng, Ph.D, MD, Alameda County Medical Center/Highland Hospital, Oakland, California, USA, from Doody's Book ReviewsTM

Since the first bacterial genome, Haemophilus influenzae, was fully sequenced in 1995, over 1000 complete bacterial genome sequences have been determined. DNA sequencing technology has dramatically improved from the first generation, automated Sanger DNA sequencing, which dominated this field for almost two decades, to the current Next-generation sequencing protocols. This newer technology dramatically reduces both the time and cost of DNA sequencing, making it possible for a small laboratory to completely sequence the genome of their favorite bacterium. With the enormous amount of information obtained from whole genome sequencing, scientists can readily address a wide range of biological questions that were hitherto beyond their capabilities. In this chapter, strategies of how to sequence genomic DNA as well as how to assemble and annotate a bacterial genome are reviewed and discussed. Keywords bacterial genomics; next generation sequencing; de novo assembly; bacterial genome annotation 1.Genome sequencing As of May 2010, 1,072 complete published bacterial genomes have been reported in the Genomes Online Database and another 4,289 bacterial genome projects are known to be ongoing (www.genomesonline.org). The underlying reasons for sequencing the genome of various bacteria are either because they are highly virulent to humans, animals or plants, or they can be applied to bioremediation or bioenergy production. In 2009, a new initiative called 'Genomic Encyclopedia of Bacteria and Archaea' (GEBA) was reported by Eisen and colleagues [1]. The project aims to provide a more complete picture of bacterial and archaeal genomic diversity by systematically filling in the gaps in the tree of life [1, 2]. With the assistance of continuously evolving DNA sequencing technologies, the goal of generating reference genomes for every major and minor group of bacteria should be achieved in the near future.

Asia Nosheen
Asghari Bano
Faizan Ullah

Comparative evaluation of plant growth promoting rhizobacteria viz. Azospirillum brasilense, Azotobacter vinelandii Khsr1 and chemical fertilizers was made on growth, protein, and oil yield as well as quality of canola (Brassica napus L.) cv. Rainbow. The A. brasilense and A. vinelandii were applied as seed inoculation at 106 cells/mL. The recommended doses of urea (150 kg/ha) and diamonium phosphate (180 kg/ha) were applied as sources of chemical fertilizers. First dose of chemical fertilizers was applied at the time of sowing while other three doses were applied at 45 days interval. The chemical fertilizers were highly effective in increasing leaf chlorophyll content, number of branches per plant, number of siliqua per branch, number of seeds per siliqua, and total seed yield. A. brasilense treatment increased the leaf and seed protein content (32 and 21%) as well as seed size as measured by % increase in 1000 seed weight. A. vinelandii treatment resulted in significant increase (4%) in seed oil contents but the glucosinolate and erucic acid (C22:1) contents of oil was decreased significantly. Maximum oleic acid (C18:1) content was found in seed oil of A. vinelandii treatment; whereas, significantly higher linolenic acid (C18:3) content was recorded in A. brasilense treatment. It is inferred from the present investigation that A. brasilense and A. vinelandii could be highly effective in improving yield and nutritive value of canola oil.

Manfred T. Reetz

Enzymes as catalysts in synthetic organic chemistry gained importance in the latter half of the 20th century, but nevertheless suffered from two major limitations. Firstly, many enzymes were not accessible in large enough quantities for practical applications. The advent of recombinant DNA technology changed this dramatically in the late 1970s. Secondly, many enzymes showed a narrow substrate scope, often poor stereo- and/or regioselectivity and/or insufficient stability under operating conditions. With the development of directed evolution in the 1990s, all of these problems can be addressed and generally solved. The present Perspective focuses on these and other developments which have popularized enzymes as part of the toolkit of synthetic organic chemists and biotechnologists. Included is a discussion of the scope and limitation of cascade reactions using enzyme mixtures in vitro and of metabolic engineering of pathways in cells as factories for the production of simple compounds such as biofuels and complex natural products. Future trends and problems are also highlighted, as is the discussion concerning biocatalysis versus nonbiological catalysis. This Perspective does not constitute a comprehensive review, and therefore the author apologizes to those researchers whose work is not specifically treated here.

Dennis R. Heldman

Fermentations occur when microorganisms consume susceptible organic substrates as part of their own metabolic processes. Such interactions are fundamental to the decomposition of natural materials, and to the ultimate return of chemical elements to the soil and air without which life could not be sustained.

Li
Xiaogang Luo
Shengjun Hu

This brief outlines the most recent advances in the production of polyols and polyurethanes from renewable resources, mainly vegetable oils, lignocellulosic biomass, starch, and protein. The typical processes for the production of polyols from each of the above mentioned feedstocks are introduced and the properties of the resultant polyols and polyurethanes are also discussed.

Background: Oysters have important ecological functions in their natural environment, acting as global carbon sinks and improving water quality by removing excess nutrients from the water column. During their life-time oysters are exposed to a variety of pathogens that can cause severe mortality in a range of oyster species. Environmental stressors encountered in their habitat can increase the susceptibility of oysters to these pathogens and in general have been shown to impact on oyster immunity, making immune parameters expressed in these marine animals an important research topic. Results: Paired-end Illumina high throughput sequencing of six S. glomerata tissues exposed to different environmental stressors resulted in a total of 484,121,702 paired-end reads. When reads and assembled transcripts were compared to the C. gigas genome, an overall low level of similarity at the nucleotide level, but a relatively high similarity at the protein level was observed. Examination of the tissue expression pattern showed that some transcripts coding for cathepsins, heat shock proteins and antioxidant proteins were exclusively expressed in the haemolymph of S. glomerata, suggesting a role in innate immunity. Furthermore, analysis of the S. glomerata ORFs showed a wide range of genes potentially involved in innate immunity, from pattern recognition receptors, components of the Toll-like signalling and apoptosis pathways to a complex antioxidant defence mechanism. Conclusions: This is the first large scale RNA-Seq study carried out in S. glomerata, showing the complex network of innate immune components that exist in this species. The results confirmed that many of the innate immune system components observed in mammals are also conserved in oysters; however, some, such as the TLR adaptors MAL, TRIF and TRAM are either missing or have been modified significantly. The components identified in this study could help explain the oysters' natural resilience against pathogenic microorganisms encountered in their natural environment.

Mehrdad Dirin
Johannes Winkler

As for any drug, tissue distribution is one of the key factors for therapeutic success of antisense oligonucleotides. This chapter summarizes the factors affecting distribution of antisense oligonucleotides and describes how distribution is a function of delivery route and affinity to plasma proteins, cells, and tissues. The principles underlying the metabolism, the enzymes involved, and the role of the metabolism on clearance of antisense oligonucleotides are discussed. This chapter also reviews the factors influencing the rate of antisense oligonucleotides metabolism such as backbone chemistry, plasma protein binding, and sequence composition and length.

Sharna-kay Daley
Geoffrey A. Cordell

The profound interconnectedness of the sciences and technologies embodied in the Fourth Industrial Revolution is discussed in terms of the global role of natural products, and how that interplays with the development of sustainable and climate-conscious practices of cyberecoethnopharmacolomics within the Quintuple Helix for the promotion of a healthier planet and society.

A METHOD FOR PRODUCING AN L-AMINO ACID USING A BACTERIUM OF THE FAMILY ENTEROBACTERIACEAE HAVING A DISRUPTED PUTRESCINE DEGRADATION PATHWAY

Herein, results of photoinduced pH oscillatory phenomena of microalgae in laboratory systems are presented. Microalgae are an extremely complex biomaterial in which light‐induced quantum mechanical processes induce changes in the surrounding aqueous environment (medium). A phenomenological understanding of the photoresponse by a quantitative study of pH oscillations of the medium is provided. The biochemical processes of algal metabolism and photosynthesis and the impact of light on a nitrate‐enriched medium are examined. pH variations in the external medium and the impact on future applications of microalgae are presented. External pH dominantly impacts conductivity in the solution of algal biophotovoltaic devices. This is the first dynamic study of the light‐induced pH behavior of microalgae with direct relevance to carbon capture, biophotovoltaic electricity generation, and quantum photosynthesis. Herein, the photoresponse of microalgae systems via unique time‐dependent pH oscillatory phenomena is presented. The goal of this research is to understand the dynamics of photosynthetic biomaterials in large controlled biochemical systems. It intends to provide applications in areas ranging from carbon capture to biophotovoltaics and rapid phenomenological methods for the study of quantum photosynthesis.

Akuakultur secara global didefinisikan FAO sebagai "usaha budidaya organisme air termasuk ikan, moluska, krustasea, dan tanaman air secara terkontrol yang bertujuan untuk meningkatkan produksi, dimiliki, dan diusahakan oleh individu atau badan usaha". Indonesia mengadopsi definisi FAO ini di mana padanan kata "akuakultur" adalah "budidaya ikan" yang didefinisikan sebagai "kegiatan untuk memelihara, membesarkan, dan atau membiakkan ikan serta memanen hasilnya dalam lingkungan terkontrol termasuk kegiatan transportasi, penyimpanan, pengolahan, dan pengawetan (UU Perikanan No. 45/2009). Kedua definisi ini secara jelas memisahkan perikanan budidaya dari perikanan tangkap melalui frase-frase "budidaya organisme air", "lingkungan terkontrol", dan "individu dan badan usaha". Dalam perikanan budidaya, frase "individu dan badan usaha" merujuk kepada perorangan atau badan usaha yang mengelola seluruh atau sebagian aktivitas pemeliharaan ikan dan sampai dengan memanen hasilnya. Definisi perikanan budidaya ini akan berubah arti menjadi perikanan tangkap jika produk akhir dari sistem tersebut atau panen dilakukan secara terbuka oleh masyarakat. Contoh kongkritnya adalah jika dalam suatu badan air, seperti waduk, ditebar dengan benih ikan budidaya dalam bentuk ranching yang hasilnya bisa diambil oleh siapa saja (open access), maka sistem ini dikategorikan sebagai perikanan tangkap dan bukan perikanan budidaya (Edwards dan Demaine, 1997). Pembedaan konsep antara perikanan budidaya dan tangkap ini masih menjadi bahan perbedaan pendapat di diskusi ruang-ruang akademis dan publik. Hal ini terutama terjadi untuk beberapa spesies ikan yang masing mengandalkan benih dari alam (napoleon dan kerapu). Dengan merujuk pada definisi Edwards dan Demaine (1997), jenis-jenis ikan tersebut yang telah mengalami masa pemeliharaan di ruang/media budidaya dan akses panennya dikontrol oleh individu atau badan usaha dapat dikategorikan sebagai ikan budidaya. Persamaan persepsi tentu saja perlu dilakukan antar pemangku kepentingan terkait lama pemeliharaan atau fase hidup ikan untuk konsistensi pengkategorian ikan hasil budidaya atau penangkapan.

Metabolic engineering involves advantageous manipulations in the metabolic pathways of suitable organisms for better yield of valuable metabolites like pharmaceuticals, fuels, dairy products, and cosmetics. In classical approach, cellular metabolism is altered by changing enzyme kinetics or regulatory proteins by employing genetic engineering tools, thus enhancing the yield of a metabolite or producing a novel bio-product. Several strategies like upregulation/downregulation of key enzymes, elimination of toxic by-products, removing feedback inhibition, reducing competition, and engineering transporters/co-factors may be employed to optimize an engineered process in suitable host like bacteria. In this chapter, a broad overview of metabolic engineering is presented, describing various strategies of metabolic engineering, plant metabolic engineering, microbial metabolic engineering with evident examples and challenges of metabolic engineering.

Brice Wilson
Christopher C Thornburg
Curtis J. Henrich
Barry R O'Keefe

Covering: up to 2020 The National Cancer Institute of the United States (NCI) has initiated a Cancer Moonshot program entitled the NCI Program for Natural Product Discovery. As part of this effort, the NCI is producing a library of 1 000 000 partially purified natural product fractions which are being plated into 384-well plates and provided to the research community free of charge. As the first 326 000 of these fractions have now been made available, this review seeks to describe the general methods used to collect organisms, extract those organisms, and create a prefractionated library. Importantly, this review also details both cell-based and cell-free bioassay methods and the adaptations necessary to those methods to productively screen natural product libraries. Finally, this review briefly describes post-screen dereplication and compound purification and scale up procedures which can efficiently identify active compounds and produce sufficient quantities of natural products for further pre-clinical development.

Mohammad Aref Kyyaly

Are genetically engineered organisms bad for biodiversity? Why is this so? There is a number of reasons standing behind this idea. In this paper, it is present two different examples from my own work about using microorganisms for production of certain enzymes for medical purposes using genetic engineering, and for treatment and protection from iron deficiency anaemia using biotechnology.

Manfred T. Reetz

Enzymes have been used as catalysts in organic chemistry for more than a century. The use of biocatalysis in academia and, particularly, in industry has some of the limitations such as limited substrate scope, insufficient activity, insufficient or wrong stereoselectivity, insufficient or wrong regioselectivity, and insufficient robustness under operating conditions. Product inhibition also limits the use of enzymes. All of these problems can be addressed and generally solved by applying directed evolution. The extensive area of evolved enzymes as catalysts in synthetic organic and pharmaceutical chemistry as well as biotechnology, applications extend into an array of very different areas, namely: metabolic pathway engineering, engineered CRISPR-Cas9 nucleases, vaccine production, potential universal blood generation, and engineered antibodies. Directed evolution is thus an alternative to so-called "rational design" in which the researcher utilizes structural, mechanistic, and sequence information, possibly flanked by computational aids, in order to perform site-directed mutagenesis at a given position in a protein.

Mohammad Aref Kyyaly

Johannes F. Buyel

Plants were the first sources of medicines used by humankind, with evidence of herbal remedies dating back at least 60,000 years. Many plants have been used medicinally because they produce secondary metabolites with pharmacological properties, including compounds such as paclitaxel (Taxol) that inhibit cell division and can therefore be used as a treatment for cancer. With the advent of recombinant DNA and molecular biotechnology in the 1970s, plants have also been modified genetically to produce more of their native pharmaceutically active substances, or even nonnative compounds. The scope of medicinal plants has also expanded beyond secondary metabolites to include pharmaceutical recombinant proteins, such as human antibodies. This chapter provides an overview of the anticancer compounds naturally produced in plants and how gene technology has been used to facilitate their production. It also considers how plant-based expression systems can help to supply modern healthcare systems with protein-based anticancer compounds such as monoclonal antibodies, lectins, and anticancer vaccines.

The production of chiral compounds as single enantiomers in the synthesis of drugs and intermediates is extremely important to the pharmaceutical industry. Due to the stereoselective interactions of a chiral drug with optically active biological macromolecules, two stereoisomeric compounds tend to differ in their pharmacokinetic/pharmacodynamic properties. Indeed, enantiomeric discrimination displayed by metabolizing enzymes often results in a preference for one enantiomer of a chiral drug. Biocatalysis involves the use of enzymes or whole cells that contain the desired enzyme or enzyme system as catalysts for chemical reactions. Baeyer-Villiger oxidation, double bond epoxidation and heteroatom oxidation also fall within the scope of this class of enzyme. As they catalyze redox processes, many of these reactions are freely reversible, and indeed oxidoreductases can also promote the reduction of aldehydes, ketones, carboxylic acids, and double and triple carbon-carbon bonds as well. Biocatalysts are also efficient promoters of synthetically useful carbon-carbon and carbonheteroatom bond-forming reactions.

Matthew D. Smith

Production of heterologous proteins in plants has become increasingly efficient due to recent advances in plant biotechnology. Heterologous proteins that have specifically attracted a great deal of attention are plant-produced monoclonal antibodies. A variety of applications for these so-called plantibodies have been explored since they were first expressed in tobacco seven years ago. Both full length antibodies and antibody fragments produced in transgenic plants offer many intriguing possibilities to plant molecular biologists and plant breeders. However, questions such as how cellular targeting influences the expression and accumulation of these proteins in plants still need to be answered before the technology can be used commercially, on a large-scale.

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Source: https://www.researchgate.net/publication/345723386_Molecular_Biotechnology_Principles_and_Applications_of_Recombinant_DNA_Fifth_Edition