#Cell cycle: Continuous chromatin changes

[legendaryturtletheorist]

Unlocking the Potential of Putrescine in Cell Culture: A Comprehensive Overview

Cell culture, a cornerstone of modern biology and biotechnology, relies on a complex interplay of various factors to ensure the growth, health, and productivity of cells. One crucial component that often goes unnoticed but plays a pivotal role is putrescine. Putrescine, a small organic compound, has been gaining recognition for its multifaceted roles in cell culture systems. In this article, we delve into the world of putrescine, exploring its significance, applications, and the science behind its influence on cell culture.

Understanding Putrescine

Putrescine, chemically known as 1,4-diaminobutane, is a diamine compound with a simple structure. It is one of the polyamines, a group of organic molecules that includes spermine and spermidine. Polyamines are essential for cell growth, and putrescine, in particular, is considered a primary precursor for the biosynthesis of higher polyamines like spermine and spermidine.

The Role of Putrescine in Cell Culture

Cell Proliferation: Putrescine is intimately involved in cell proliferation. It facilitates DNA synthesis by acting as a cofactor for several enzymes, ensuring that cells can replicate their genetic material accurately during the cell cycle.

Antioxidant Properties: Putrescine has antioxidant properties, which means it helps protect cells from oxidative stress and damage caused by reactive oxygen species (ROS). This property can be particularly valuable in maintaining healthy cell cultures, as oxidative stress can hinder cell growth and viability.

Regulation of Gene Expression: Putrescine can modulate gene expression by influencing chromatin structure and gene transcription. This can lead to changes in the expression of genes related to cell growth, differentiation, and apoptosis, making it a critical player in cell culture systems.

Stress Response: Cells in culture can experience various forms of stress, such as nutrient depletion or exposure to toxins. Putrescine helps cells adapt to these stressors and enhances their survival under adverse conditions.

Applications of Putrescine in Cell Culture

The applications of putrescine in cell culture are diverse and impactful. Here are some key areas where it finds utility:

Cancer Research: Putrescine is often used in cancer cell culture studies. Its involvement in cell proliferation and gene expression makes it relevant for understanding cancer cell behavior and potential therapeutic targets.

Stem Cell Culture: Stem cells are crucial for regenerative medicine and tissue engineering. Putrescine can play a role in optimizing the culture conditions for these cells, promoting their expansion and differentiation.

Vaccine Production: The production of vaccines often involves growing cells in culture. Putrescine can enhance cell growth and protein expression, making it beneficial for vaccine development.

Bioprocessing: In bioprocessing and biomanufacturing, putrescine can be used to improve the productivity of cell lines used to produce biopharmaceuticals and other bioproducts.

Neuroscience Research: Researchers studying neuronal cells can utilize putrescine to support cell growth and differentiation, aiding in neurobiology experiments and drug development.

Challenges and Considerations

While putrescine offers numerous advantages in cell culture, there are also challenges to consider. Excessive putrescine levels can be toxic to cells, so careful optimization of its concentration in culture media is essential. Additionally, putrescine should be stored and handled with care, as it is sensitive to environmental factors like pH and temperature.

In conclusion

putrescine cell culture is a small molecule with significant implications in cell culture systems. Its roles in cell proliferation, gene expression, and stress response make it a valuable tool in various fields of research and biotechnology. As scientists continue to explore its potential, we can anticipate even more applications and a deeper understanding of its influence on cell culture in the future. Harnessing the power of putrescine may open new doors for advancements in cellular biology and bioprocessing.

[wisdomrays]

TAFAKKUR: Part 184

Recurring DNA in Genome Structure: Part 1

A genome is a data book or registry which records the past and future of living organisms. It dynamically and simultaneously stores hereditary and biological information in three different hierarchical levels belonging to three different time periods.

The first is the preservation of characteristic, long term data imprints that describes the development of an organism in the stable DNA sequences.

Second is the storage of medium term epigenetically featured data that is carried a couple of generations further down the cellular level. Epigenetic information is not stored within nucleotide sequences but in the chemical modifications of these sequences (like the methylation of repeated strings of GC dinucleotide).

Third is the storage of data generated as a result of dynamic interactions between proteins, RNA and DNA in order to adapt to the events and changes during cellular life cycle in the form of nucleoprotein or DNA-protein complexes.

The data generation and storage capacity of DNA in three different hierarchical levels and time periods demonstrates that genome plays a plethora of roles in cellular activities and heredity. Formatting of genome for its generation and storage of data is carried out via DNA sequences of various features. Genomic system is composed of repeating DNA sequences. DNA sequences (satellite) function as a marker as they repeat numerous times in various frequencies. Genome includes genomic folders similar to that of computer systems. These genomic folders, also known as the epigenetic index of genomes, are responsible for the remodeling of chromatin and the coordinated control of genomic functions. Repeating DNA sequences play a critical role in replication of genome (making a copy of DNA), dispersal of copied DNA into daughter cells and construction of support systems that enable organization of chromatins.

It is possible to better understand genomic functions in relation to examples such as memory sticks and hard drives that are used in electronic information systems. The difference between a genome as a basic data-information storage medium from a hard disc is that it can be replicated as required by its nature and these replicas can be transferred to daughter cells. Following examples could be given to illustrate that a genome gains function only when it interacts with various data processing modules in the cell.

A copy of genome is produced by cellular DNA replication system

Correct localization of each genome copy towards daughter cells is only possible when chromosome segregation system works (the centrosomes and microtubules)

The central transcription system is responsible for the copy of data from DNA to RNA. Different gene expression patterns are developed via regulation of transcription time and level with the help of transcription factors and a web of cell signalization.

Very intricately organized genomic system structures are designed through the successive combination of protein encoding sequences, signals distributed in various places and repeating DNA sequences. Formatting of genome resembles formatting of computer programs. Various repeated serial commands of computer software are used to allocate addresses to files independent of the original data contained; different computer systems use different signals and structures to manage programs. In a similar fashion, diverse living species often utilize repeating DNA sequences and chromosomal structures to organize the encoded information and to format their genomes.

Diversity and variation of repeating DNA sequences are building blocks that are constructed into different genomic system structures. Genomes of different organisms bear characteristic system morphology just like computers with various operating systems and hardware. For instance, animal cells are created as a good model to take and incorporate foreign DNA into their genomes. Genetic data transfer among organisms of the same kind is referred to as “vertical gene transfer” whereas transfers between different species, genuses and classes are called “horizontal gene transfer.” Mobile DNA sequences like transposons are very effective horizontal gene transfer agents.

Cellular differentiation and morphogenesis (formation of tissue and organ from cell) is not programmed completely in the primary structure of the DNA sequence. Components of modular programs are encoded in a flexible way and a continuous renewed and recombined arrangement is enabled when needed.

The reason behind creation of different organisms from a single genome is this utilization of such genomic structure. Metamorphosis, that is the development of different organisms like invertebrates such as a caterpillar and a butterfly, is a good example of this feature.

Two organisms from the perspective of the same genomic protein and RNA codes can be considered as two different species. Different genomic structures and repetition of sequences among different organisms are distinctive criteria for the identification of species since these features can lead to mismatch of reproductive cells, different expression patterns of genetic code sequences, and may cause ecological diversity as well. That is why repeated DNA sequences are very important in studying parental relationships. Today, microsatellite DNA as repeated DNA sequences are used to configure biological relations among individuals in forensic sciences. Plant species vary in respect to the repeated sequences in centromeres in their chromosomes; these variations are used for identification of species. Main determinants of genomic system structure are diversity, frequency, and genomic localization of repeated DNA sequences. To explain this with examples, we could say that successively repeated sequences at centromeres, telomere repetitions and transcription, packing of chromatin, repeated sequences that are spread throughout genome in charge of cellular functions like nucleus localization are the main elements of the genome system structure. Genome is a single integrated system that is controlled closely and remotely via communication webs that use repeated sequences.

While explaining the Qur’anic concept of the Manifest Record (36:12) Bediuzzaman Said Nursi, the great renovator of Islamic thought in Turkey in the twentieth century, wrote that the Manifest Record expresses one aspect of Divine knowledge that is related “more to the past and future than to the present. It is a book of Divine Destiny that contains the origins, roots, and seeds of things, rather than their flourishing forms in their visible existence” (30th Word, Second Aim).

Inspired from this view, a seed can be considered as a tiny adorned form of Divinely creative command as programs and indexes and as a determinant for those programs and indexes in the organization of an entire tree. Since the Manifest Record book, as a title of Divine knowledge and command, observes the past and the future rather than the present, the genome of a grain or a seed acts like a library and an archive in which the future and past of an organism is written.

[toppersexam]

GATE Life Science Question Paper, Exam Pattern, Mock Test, MCQ

GATE Life Science Question Paper, Exam Pattern, Mock Test, MCQ The Graduate Aptitude Test in Engineering is an examination that primarily tests the comprehensive understanding of various undergraduate subjects in engineering and science for admission into the Masters Program of institutes as well as jobs at Public Sector Companies. GATE Life Science Question Paper and MCQs Buy the question bank or online quiz of GATE Life Science Exam Going through the GATE Life Science Exam Question Bank is a must for aspirants to both understand the exam structure as well as be well prepared to attempt the exam. The first step towards both preparation as well as revision is to practice from GATE Life Science Exam with the help of Question Bank or Online quiz. We will provide you the questions with detailed answer. GATE Life Science Question Paper and MCQs : Available Now GATE Life Science Mock Test Crack GATE Life Science Recruitment exam with the help of online mock test Series or Free Mock Test. Every Sample Paper in GATE Life Science Exam has a designated weightage so do not miss out any Paper. Prepare and Practice Mock for GATE Life Science exam and check your test scores. You can get an experience by doing the Free Online Test or Sample Paper of GATE Life Science Exam. Free Mock Test will help you to analysis your performance in the Examination. GATE Life Science Mock Test : Available Now GATE Life Science Syllabus 1. Chemistry (Compulsory) : Atomic structure and periodicity: Planck’s quantum theory, wave particle duality, uncertainty principle, quantum mechanical model of hydrogen atom, electronic configuration of atoms and ions. Periodic table and periodic properties: ionization energy, electron affinity, electronegativity and atomic size. Structure and bonding: Ionic and covalent bonding, MO and VB approaches for diatomic molecules, VSEPR theory and shape of molecules, hybridization, resonance, dipole moment, structure parameters such as bond length, bond angle and bond energy, hydrogen bonding and van der Waals interactions. Ionic solids, ionic radii and lattice energy (Born‐Haber cycle). HSAB principle. s.p. and d Block Elements: Oxides, halides and hydrides of alkali, alkaline earth metals, B, Al, Si, N, P, and S. General characteristics of 3d elements. Coordination complexes: valence bond and crystal field theory, color, geometry, magnetic properties and isomerism. Chemical Equilibria: Colligative properties of solutions, ionic equilibria in solution, solubility product, common ion effect, hydrolysis of salts, pH, buffer and their applications. Equilibrium constants (Kc, Kp and Kx) for homogeneous reactions. Electrochemistry: Conductance, Kohlrausch law, cell potentials, emf, Nernst equation, Galvanic cells, thermodynamic aspects and their applications. Reaction Kinetics: Rate constant, order of reaction, molecularity, activation energy, zero, first and second order kinetics, catalysis and elementary enzyme reactions. Thermodynamics: First law, reversible and irreversible processes, internal energy, enthalpy, Kirchoff equation, heat of reaction, Hess’s law, heat of formation. Second law, entropy, free energy and work function. Gibbs‐Helmholtz equation, Clausius‐Clapeyron equation, free energy change, equilibrium constant and Trouton’s rule. Third law of thermodynamics Plant Pathology: Nature and classification of plant diseases, diseases of important crops caused by fungi, bacteria,nematodes and viruses, and their control measures, mechanism(s) of pathogenesis and resistance, molecular detection of pathogens; plant-microbe beneficial interactions. Ecology and Environment: Ecosystems – types, dynamics, degradation, ecological succession; food chains and energy flow; vegetation types of the world, pollution and global warming, speciation and extinction, conservation strategies, cryopreservation, phytoremediation. 3. Microbiology Historical Perspective: Discovery of microbial world; Landmark discoveries relevant to the field of microbiology; Controversy over spontaneous generation; Role of microorganisms in transformation of organic matter and in the causation of diseases. Methods in Microbiology: Pure culture techniques; Theory and practice of sterilization; Principles of microbial nutrition; Enrichment culture techniques for isolation of microorganisms; Light-, phase contrast- and electron-microscopy. Microbial Taxonomy and Diversity: Bacteria, Archea and their broad classification; Eukaryotic microbes: Yeasts, molds and protozoa; Viruses and their classification; Molecular approaches to microbial taxonomy. Prokaryotic and Eukaryotic Cells: Structure and Function: Prokaryotic Cells: cell walls, cell membranes, mechanisms of solute transport across membranes, Flagella and Pili, Capsules, Cell inclusions like endospores and gas vesicles; Eukaryotic cell organelles: Endoplasmic reticulum, Golgi apparatus, mitochondria and chloroplasts. Microbial Growth: Definition of growth; Growth curve; Mathematical expression of exponential growth phase; Measurement of growth and growth yields; Synchronous growth; Continuous culture; Effect of environmental factors on growth. Control of Micro-organisms: Effect of physical and chemical agents; Evaluation of effectiveness of antimicrobial agents. Microbial Metabolism: Energetics: redox reactions and electron carriers; An overview of metabolism; Glycolysis; Pentose-phosphate pathway; Entner-Doudoroff pathway; Glyoxalate pathway; The citric acid cycle; Fermentation; Aerobic and anaerobic respiration; Chemolithotrophy; Photosynthesis; Calvin cycle; Biosynthetic pathway for fatty acids synthesis; Common regulatory mechanisms in synthesis of amino acids; Regulation of major metabolic pathways. Microbial Diseases and Host Pathogen Interaction: Normal microbiota; Classification of infectious diseases; Reservoirs of infection; Nosocomial infection; Emerging infectious diseases; Mechanism of microbial pathogenicity; Nonspecific defense of host; Antigens and antibodies; Humoral and cell mediated immunity; Vaccines; Immune deficiency; Human diseases caused by viruses, bacteria, and pathogenic fungi. Chemotherapy/Antibiotics: General characteristics of antimicrobial drugs; Antibiotics: Classification, mode of action and resistance; Antifungal and antiviral drugs. Microbial Genetics: Types of mutation; UV and chemical mutagens; Selection of mutants; Ames test for mutagenesis; Bacterial genetic system: transformation, conjugation, transduction, recombination, plasmids, transposons; DNA repair; Regulation of gene expression: repression and induction; Operon model; Bacterial genome with special reference to E.coli; Phage λ and its life cycle; RNA phages; RNA viruses; Retroviruses; Basic concept of microbial genomics. Microbial Ecology: Microbial interactions; Carbon, sulphur and nitrogen cycles; Soil microorganisms associated with vascular plants. 4. Zoology Animal world: Animal diversity, distribution, systematics and classification of animals, phylogenetic relationships. Evolution: Origin and history of life on earth, theories of evolution, natural selection, adaptation, speciation. Genetics: Basic Principles of inheritance, molecular basis of heredity, sex determination and sex-linked characteristics, cytoplasmic inheritance, linkage, recombination and mapping of genes in eukaryotes, population genetics. Biochemistry and Molecular Biology: Nucleic acids, proteins, lipids and carbohydrates; replication, transcription and translation; regulation of gene expression, organization of genome, Kreb’s cycle, glycolysis, enzyme catalysis, hormones and their actions, vitamins Cell Biology: Structure of cell, cellular organelles and their structure and function, cell cycle, cell division, chromosomes and chromatin structure. Gene expression in Eukaryotes : Eukaryotic gene organization and expression (Basic principles of signal transduction). Animal Anatomy and Physiology: Comparative physiology, the respiratory system, circulatory system, digestive system, the nervous system, the excretory system, the endocrine system, the reproductive system, the skeletal system, osmoregulation. Parasitology and Immunology: Nature of parasite, host-parasite relation, protozoan and helminthic parasites, the immune response, cellular and humoral immune response, evolution of the immune system. Development Biology: Embryonic development, cellular differentiation, organogenesis, metamorphosis, genetic basis of development, stem cells. Ecology: The ecosystem, habitats, the food chain, population dynamics, species diversity, zoogerography, biogeochemical cycles, conservation biology. Animal Behaviour: Types of behaviours, courtship, mating and territoriality, instinct, learning and memory, social behaviour across the animal taxa, communication, pheromones, evolution of animal behaviour. GATE 2021 LX Exam Pattern Duration : 180 Mint Negative Mark : 0.66 SectionNo. of QuestionsMarksMarks/QuestionsTotal Marks General Aptitude5 55 51 25 10 Technical, Engineering, Mathematics25 3025 301 225 60 Total65  100

[naivelocus]

Cell cycle: Continuous chromatin changes

Cell cycle: Continuous chromatin changes

Nature 547, 7661 (2017). doi:10.1038/547034a

Authors: Robert A. Beagrie & Ana Pombo

DNA is packaged in the cell as chromatin, which folds into organized domains. Mapping of chromatin contacts in single cells sheds light on the dynamic evolution of these domains between cell divisions. See Article p.61

— Nature - Issue - nature.com scie...

[abbkineeu]

New Post has been published on Biotech Advisers

New Post has been published on http://www.bioadvisers.com/weekly-top-scientific-research-review-852017-1252017/

Weekly Top Scientific Research Review (8/5/2017-12/5/2017)

Here we start our beautiful journey!

1. CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR–Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here Tyler S Klann at Duke University in Durham, North Carolina, USA and his colleagues describe CRISPR–Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9KRAB repressor and dCas9p300 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, they carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context, the authors suggest.

Read more, please click http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3853.html

2. A living mesoscopic cellular automaton made of skin scales.

In vertebrates, skin colour patterns emerge from nonlinear dynamical microscopic systems of cell interactions. Here Liana Manukyan at University of Geneva in Geneva, Switzerland and his colleagues show that in ocellated lizards a quasi-hexagonal lattice of skin scales, rather than individual chromatophore cells, establishes a green and black labyrinthine pattern of skin colour. They analysed time series of lizard scale colour dynamics over four years of their development and demonstrate that this pattern is produced by a cellular automaton (a grid of elements whose states are iterated according to a set of rules based on the states of neighbouring elements) that dynamically computes the colour states of individual mesoscopic skin scales to produce the corresponding macroscopic colour pattern. Using numerical simulations and mathematical derivation, they identify how a discrete von Neumann cellular automaton emerges from a continuous Turing reaction–diffusion system. Skin thickness variation generated by three-dimensional morphogenesis of skin scales causes the underlying reaction–diffusion dynamics to separate into microscopic and mesoscopic spatial scales, the latter generating a cellular automaton. Their study indicates that cellular automata are not merely abstract computational systems, but can directly correspond to processes generated by biological evolution.

Read more, please click http://www.nature.com/nature/journal/v544/n7649/full/nature22031.html

3. Virus genomes reveal factors that spread and sustained the Ebola epidemic.

The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here Gytis Dudas at University of Edinburgh in Edinburgh, UK and his colleagues reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. They test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic ‘gravity’ model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. They address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, they reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Read more, please click http://www.nature.com/nature/journal/v544/n7650/full/nature22040.html

4. Structure and allosteric inhibition of excitatory amino acid transporter 1.

Human members of the solute carrier 1 (SLC1) family of transporters take up excitatory neurotransmitters in the brain and amino acids in peripheral organs. Dysregulation of the function of SLC1 transporters is associated with neurodegenerative disorders and cancer. Here Juan C. Canul-Tec at  Institut Pasteur in Paris, France and his colleagues present crystal structures of a thermostabilized human SLC1 transporter, the excitatory amino acid transporter 1 (EAAT1), with and without allosteric and competitive inhibitors bound. The structures reveal architectural features of the human transporters, such as intra- and extracellular domains that have potential roles in transport function, regulation by lipids and post-translational modifications. The coordination of the allosteric inhibitor in the structures and the change in the transporter dynamics measured by hydrogen–deuterium exchange mass spectrometry reveal a mechanism of inhibition, in which the transporter is locked in the outward-facing states of the transport cycle. Their results provide insights into the molecular mechanisms underlying the function and pharmacology of human SLC1 transporters.

Read more, please click http://www.nature.com/nature/journal/vaop/ncurrent/full/nature22064.html

5. Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson’s disease model.

Cell replacement therapies for neurodegenerative disease have focused on transplantation of the cell types affected by the pathological process. Here Pia Rivetti di Val Cervo at Karolinska Institutet in Stockholm, Sweden and his colleagues describe an alternative strategy for Parkinson’s disease in which dopamine neurons are generated by direct conversion of astrocytes. Using three transcription factors, NEUROD1, ASCL1 and LMX1A, and the microRNA miR218, collectively designated NeAL218, they reprogram human astrocytes in vitro, and mouse astrocytes in vivo, into induced dopamine neurons (iDANs). Reprogramming efficiency in vitro is improved by small molecules that promote chromatin remodeling and activate the TGFβ, Shh and Wnt signaling pathways. The reprogramming efficiency of human astrocytes reaches up to 16%, resulting in iDANs with appropriate midbrain markers and excitability. In a mouse model of Parkinson’s disease, NeAL218 alone reprograms adult striatal astrocytes into iDANs that are excitable and correct some aspects of motor behavior in vivo, including gait impairments. With further optimization, this approach may enable clinical therapies for Parkinson’s disease by delivery of genes rather than cells.

Read more, please click http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3835.html

[bioadvisers]

New Post has been published on Biotech Advisers

New Post has been published on http://www.bioadvisers.com/weekly-top-scientific-research-review-852017-1252017/

Weekly Top Scientific Research Review (8/5/2017-12/5/2017)

Here we start our beautiful journey!

1. CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR–Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here Tyler S Klann at Duke University in Durham, North Carolina, USA and his colleagues describe CRISPR–Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9KRAB repressor and dCas9p300 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, they carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context, the authors suggest.

Read more, please click http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3853.html

2. A living mesoscopic cellular automaton made of skin scales.

In vertebrates, skin colour patterns emerge from nonlinear dynamical microscopic systems of cell interactions. Here Liana Manukyan at University of Geneva in Geneva, Switzerland and his colleagues show that in ocellated lizards a quasi-hexagonal lattice of skin scales, rather than individual chromatophore cells, establishes a green and black labyrinthine pattern of skin colour. They analysed time series of lizard scale colour dynamics over four years of their development and demonstrate that this pattern is produced by a cellular automaton (a grid of elements whose states are iterated according to a set of rules based on the states of neighbouring elements) that dynamically computes the colour states of individual mesoscopic skin scales to produce the corresponding macroscopic colour pattern. Using numerical simulations and mathematical derivation, they identify how a discrete von Neumann cellular automaton emerges from a continuous Turing reaction–diffusion system. Skin thickness variation generated by three-dimensional morphogenesis of skin scales causes the underlying reaction–diffusion dynamics to separate into microscopic and mesoscopic spatial scales, the latter generating a cellular automaton. Their study indicates that cellular automata are not merely abstract computational systems, but can directly correspond to processes generated by biological evolution.

Read more, please click http://www.nature.com/nature/journal/v544/n7649/full/nature22031.html

3. Virus genomes reveal factors that spread and sustained the Ebola epidemic.

The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here Gytis Dudas at University of Edinburgh in Edinburgh, UK and his colleagues reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. They test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic ‘gravity’ model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. They address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, they reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Read more, please click http://www.nature.com/nature/journal/v544/n7650/full/nature22040.html

4. Structure and allosteric inhibition of excitatory amino acid transporter 1.

Human members of the solute carrier 1 (SLC1) family of transporters take up excitatory neurotransmitters in the brain and amino acids in peripheral organs. Dysregulation of the function of SLC1 transporters is associated with neurodegenerative disorders and cancer. Here Juan C. Canul-Tec at  Institut Pasteur in Paris, France and his colleagues present crystal structures of a thermostabilized human SLC1 transporter, the excitatory amino acid transporter 1 (EAAT1), with and without allosteric and competitive inhibitors bound. The structures reveal architectural features of the human transporters, such as intra- and extracellular domains that have potential roles in transport function, regulation by lipids and post-translational modifications. The coordination of the allosteric inhibitor in the structures and the change in the transporter dynamics measured by hydrogen–deuterium exchange mass spectrometry reveal a mechanism of inhibition, in which the transporter is locked in the outward-facing states of the transport cycle. Their results provide insights into the molecular mechanisms underlying the function and pharmacology of human SLC1 transporters.

Read more, please click http://www.nature.com/nature/journal/vaop/ncurrent/full/nature22064.html

5. Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson’s disease model.

Cell replacement therapies for neurodegenerative disease have focused on transplantation of the cell types affected by the pathological process. Here Pia Rivetti di Val Cervo at Karolinska Institutet in Stockholm, Sweden and his colleagues describe an alternative strategy for Parkinson’s disease in which dopamine neurons are generated by direct conversion of astrocytes. Using three transcription factors, NEUROD1, ASCL1 and LMX1A, and the microRNA miR218, collectively designated NeAL218, they reprogram human astrocytes in vitro, and mouse astrocytes in vivo, into induced dopamine neurons (iDANs). Reprogramming efficiency in vitro is improved by small molecules that promote chromatin remodeling and activate the TGFβ, Shh and Wnt signaling pathways. The reprogramming efficiency of human astrocytes reaches up to 16%, resulting in iDANs with appropriate midbrain markers and excitability. In a mouse model of Parkinson’s disease, NeAL218 alone reprograms adult striatal astrocytes into iDANs that are excitable and correct some aspects of motor behavior in vivo, including gait impairments. With further optimization, this approach may enable clinical therapies for Parkinson’s disease by delivery of genes rather than cells.

Read more, please click http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3835.html

[abbkine]

New Post has been published on Biotech Advisers

Weekly Top Scientific Research Review (8/5/2017-12/5/2017)

Here we start our beautiful journey!

1. CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR–Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here Tyler S Klann at Duke University in Durham, North Carolina, USA and his colleagues describe CRISPR–Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9KRAB repressor and dCas9p300 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, they carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context, the authors suggest.

Read more, please click http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3853.html

2. A living mesoscopic cellular automaton made of skin scales.

In vertebrates, skin colour patterns emerge from nonlinear dynamical microscopic systems of cell interactions. Here Liana Manukyan at University of Geneva in Geneva, Switzerland and his colleagues show that in ocellated lizards a quasi-hexagonal lattice of skin scales, rather than individual chromatophore cells, establishes a green and black labyrinthine pattern of skin colour. They analysed time series of lizard scale colour dynamics over four years of their development and demonstrate that this pattern is produced by a cellular automaton (a grid of elements whose states are iterated according to a set of rules based on the states of neighbouring elements) that dynamically computes the colour states of individual mesoscopic skin scales to produce the corresponding macroscopic colour pattern. Using numerical simulations and mathematical derivation, they identify how a discrete von Neumann cellular automaton emerges from a continuous Turing reaction–diffusion system. Skin thickness variation generated by three-dimensional morphogenesis of skin scales causes the underlying reaction–diffusion dynamics to separate into microscopic and mesoscopic spatial scales, the latter generating a cellular automaton. Their study indicates that cellular automata are not merely abstract computational systems, but can directly correspond to processes generated by biological evolution.

Read more, please click http://www.nature.com/nature/journal/v544/n7649/full/nature22031.html

3. Virus genomes reveal factors that spread and sustained the Ebola epidemic.

The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here Gytis Dudas at University of Edinburgh in Edinburgh, UK and his colleagues reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. They test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic ‘gravity’ model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. They address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, they reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Read more, please click http://www.nature.com/nature/journal/v544/n7650/full/nature22040.html

4. Structure and allosteric inhibition of excitatory amino acid transporter 1.

Human members of the solute carrier 1 (SLC1) family of transporters take up excitatory neurotransmitters in the brain and amino acids in peripheral organs. Dysregulation of the function of SLC1 transporters is associated with neurodegenerative disorders and cancer. Here Juan C. Canul-Tec at  Institut Pasteur in Paris, France and his colleagues present crystal structures of a thermostabilized human SLC1 transporter, the excitatory amino acid transporter 1 (EAAT1), with and without allosteric and competitive inhibitors bound. The structures reveal architectural features of the human transporters, such as intra- and extracellular domains that have potential roles in transport function, regulation by lipids and post-translational modifications. The coordination of the allosteric inhibitor in the structures and the change in the transporter dynamics measured by hydrogen–deuterium exchange mass spectrometry reveal a mechanism of inhibition, in which the transporter is locked in the outward-facing states of the transport cycle. Their results provide insights into the molecular mechanisms underlying the function and pharmacology of human SLC1 transporters.

Read more, please click http://www.nature.com/nature/journal/vaop/ncurrent/full/nature22064.html

5. Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson’s disease model.

Cell replacement therapies for neurodegenerative disease have focused on transplantation of the cell types affected by the pathological process. Here Pia Rivetti di Val Cervo at Karolinska Institutet in Stockholm, Sweden and his colleagues describe an alternative strategy for Parkinson’s disease in which dopamine neurons are generated by direct conversion of astrocytes. Using three transcription factors, NEUROD1, ASCL1 and LMX1A, and the microRNA miR218, collectively designated NeAL218, they reprogram human astrocytes in vitro, and mouse astrocytes in vivo, into induced dopamine neurons (iDANs). Reprogramming efficiency in vitro is improved by small molecules that promote chromatin remodeling and activate the TGFβ, Shh and Wnt signaling pathways. The reprogramming efficiency of human astrocytes reaches up to 16%, resulting in iDANs with appropriate midbrain markers and excitability. In a mouse model of Parkinson’s disease, NeAL218 alone reprograms adult striatal astrocytes into iDANs that are excitable and correct some aspects of motor behavior in vivo, including gait impairments. With further optimization, this approach may enable clinical therapies for Parkinson’s disease by delivery of genes rather than cells.

Read more, please click http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3835.html

[abbkineus]

New Post has been published on Biotech Advisers

New Post has been published on http://www.bioadvisers.com/weekly-top-scientific-research-review-852017-1252017/

Weekly Top Scientific Research Review (8/5/2017-12/5/2017)

Here we start our beautiful journey!

1. CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR–Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here Tyler S Klann at Duke University in Durham, North Carolina, USA and his colleagues describe CRISPR–Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9KRAB repressor and dCas9p300 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, they carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context, the authors suggest.

Read more, please click http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3853.html

2. A living mesoscopic cellular automaton made of skin scales.

In vertebrates, skin colour patterns emerge from nonlinear dynamical microscopic systems of cell interactions. Here Liana Manukyan at University of Geneva in Geneva, Switzerland and his colleagues show that in ocellated lizards a quasi-hexagonal lattice of skin scales, rather than individual chromatophore cells, establishes a green and black labyrinthine pattern of skin colour. They analysed time series of lizard scale colour dynamics over four years of their development and demonstrate that this pattern is produced by a cellular automaton (a grid of elements whose states are iterated according to a set of rules based on the states of neighbouring elements) that dynamically computes the colour states of individual mesoscopic skin scales to produce the corresponding macroscopic colour pattern. Using numerical simulations and mathematical derivation, they identify how a discrete von Neumann cellular automaton emerges from a continuous Turing reaction–diffusion system. Skin thickness variation generated by three-dimensional morphogenesis of skin scales causes the underlying reaction–diffusion dynamics to separate into microscopic and mesoscopic spatial scales, the latter generating a cellular automaton. Their study indicates that cellular automata are not merely abstract computational systems, but can directly correspond to processes generated by biological evolution.

Read more, please click http://www.nature.com/nature/journal/v544/n7649/full/nature22031.html

3. Virus genomes reveal factors that spread and sustained the Ebola epidemic.

The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here Gytis Dudas at University of Edinburgh in Edinburgh, UK and his colleagues reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. They test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic ‘gravity’ model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. They address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, they reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Read more, please click http://www.nature.com/nature/journal/v544/n7650/full/nature22040.html

4. Structure and allosteric inhibition of excitatory amino acid transporter 1.

Human members of the solute carrier 1 (SLC1) family of transporters take up excitatory neurotransmitters in the brain and amino acids in peripheral organs. Dysregulation of the function of SLC1 transporters is associated with neurodegenerative disorders and cancer. Here Juan C. Canul-Tec at  Institut Pasteur in Paris, France and his colleagues present crystal structures of a thermostabilized human SLC1 transporter, the excitatory amino acid transporter 1 (EAAT1), with and without allosteric and competitive inhibitors bound. The structures reveal architectural features of the human transporters, such as intra- and extracellular domains that have potential roles in transport function, regulation by lipids and post-translational modifications. The coordination of the allosteric inhibitor in the structures and the change in the transporter dynamics measured by hydrogen–deuterium exchange mass spectrometry reveal a mechanism of inhibition, in which the transporter is locked in the outward-facing states of the transport cycle. Their results provide insights into the molecular mechanisms underlying the function and pharmacology of human SLC1 transporters.

Read more, please click http://www.nature.com/nature/journal/vaop/ncurrent/full/nature22064.html

5. Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson’s disease model.

Cell replacement therapies for neurodegenerative disease have focused on transplantation of the cell types affected by the pathological process. Here Pia Rivetti di Val Cervo at Karolinska Institutet in Stockholm, Sweden and his colleagues describe an alternative strategy for Parkinson’s disease in which dopamine neurons are generated by direct conversion of astrocytes. Using three transcription factors, NEUROD1, ASCL1 and LMX1A, and the microRNA miR218, collectively designated NeAL218, they reprogram human astrocytes in vitro, and mouse astrocytes in vivo, into induced dopamine neurons (iDANs). Reprogramming efficiency in vitro is improved by small molecules that promote chromatin remodeling and activate the TGFβ, Shh and Wnt signaling pathways. The reprogramming efficiency of human astrocytes reaches up to 16%, resulting in iDANs with appropriate midbrain markers and excitability. In a mouse model of Parkinson’s disease, NeAL218 alone reprograms adult striatal astrocytes into iDANs that are excitable and correct some aspects of motor behavior in vivo, including gait impairments. With further optimization, this approach may enable clinical therapies for Parkinson’s disease by delivery of genes rather than cells.

Read more, please click http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3835.html

[simplifiedbiology-blog]

New Post has been published on https://ramneetkaur.com/cell-division-mitosis-meiosis/

Cell Division - Mitosis & Meiosis

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CELL DIVISION: Mitosis & Meiosis

Cell Cycle

Can be divided into 2 stages: INTERPHASE.

G1 Growth phase 1.

S  Synthetic phase.

G2 Growth phase 2.

DIVISIONAL PHASE.

M Mitosis/Meiosis.

C Cytokinesis.

Mnemonic:“Go Sally Go! Make Children!”

  Mitosis

It is an equational division. Occurs in somatic cells.

Prophase, Metaphase, Anaphase, Telophase

Mnemonic: “People Meet And Talk”

Prophase:

Coiling of chromatin occurs, forming thin long threads.

By the end, chromosomes start forming,

Nucleolus & nuclear membrane starts disappearing by the end.

Spindle fiber formation starts.

Centriole in animal cells starts moving towards the poles.

Metaphase:

Nuclear membrane and nucleolus has disappeared,

Spindle fibers have formed, 

2 types of spindle fibers occur chromosomal fibers that are attached to chromosomes at the centromere & continuous fibers that join the 2 poles.

Chromosomes having two chromatids are seen,

Chromosomes align themselves on the equatorial plate due to contraction of spindle fibers.

Amphiastral mitosis occurs in animal cells & anastral mitosis occurs in plant cells.

Anaphase:

Shortest phase.

Centromere splits

Chromosomes start moving towards poles due to contraction of spindle fibers.

Various shapes of chromosomes are seen.

Telophase:

Chromosomes have reached the poles,

Uncoiling of chromosomes occur,

Nucleolus and nuclear membrane reappear,

Spindle fibers disappear.

2 nuclei are formed by the end.

Cytokinesis:

Starts in mid-Anaphase and ends by the end of Telophase dividing the cell into 2 daughter cells.

Occurs by invagination of the cell membrane in animal cells & by cell plate method in plant cells.

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Meiosis

It occurs in 2 stages:

Meiosis I – reductional division:

Prophase I, Metaphase I, Anaphase I, Telophase I.

Prophase I: divided into 5 substages.

Mnemonic: Little Zara in Pink Dress is Dancing.

Leptotene:

Chromatin coils forming thin long threads.

Zygotene:

Further coiling of chromatin occurs.

Pairing of homologous chromosomes occurs due to the mutual attraction between them.

Synapsis is pairing of homologous chromosomes.

Bivalents are seen.

Synaptinemal complex occurs between homologous chromosomes, that helps in precise pairing.

Pachytene:

Each chromosome splits longitudinally to form two chromatids attached at the centromere.

Bivalent changes into tetrad.

Crossing over, i.e., exchange of segments between non-sister chromatids occurs.

Crossing over occurs by the help of recombinase enzyme.

Diplotene:

Homologous chromosomes try to separate.

Chromosomes remain attached at regions where crossing over has occurred.

Chaisma is the regions where crossing over has occurred.

Chromosomes pull themselves apart from the centromere, as a result chaisma starts moving towards ends.

This is Terminalization, which starts in diplotene stage.

Diakinesis:

Terminalization completes forming ring-shaped chromosomes.

Nucleolus & nuclear membrane starts disappearing, spindle fiber formation starts.

Metaphase I:

Nucleolus & nuclear membrane has disappeared, spindle fiber formation is completed.

Chromosomes align on equatorial plate.

Anaphase I:

Homologous chromosomes separate due to contraction of spindle fibers, 

Terminal chaisma opens up & the chromosomes start moving towards poles.

Telophase I:

Chromosomes reach poles and uncoiling starts.

Nucleolus & nuclear membrane reappear, spindle fibers disappear.

Two nuclei one at each pole are formed.

Meiosis II – equational division:

Prophase II, Metaphase II, Anaphase II, Telophase II.

Meiosis II is same as Mitosis.

4 daughters cells each having haploid number of chromosomes are produced.

Also watch:Cell Cycle, Chromosomes.

Also read:

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[thetruthseekerway]

Recurring DNA in Genome Structure

New Post has been published on http://www.truth-seeker.info/quran-science-2/recurring-dna-genome-structure/

Recurring DNA in Genome Structure

By Hamza Aydin

The data generation and storage capacity of DNA in three different hierarchical levels and time periods demonstrates that genome plays a plethora of roles in cellular activities and heredity.

A genome is a data book or registry which records the past and future of living organisms. It dynamically and simultaneously stores hereditary and biological information in three different hierarchical levels belonging to three different time periods.

The first is the preservation of characteristic, long term data imprints that describes the development of an organism in the stable DNA sequences. Second is the storage of medium term epigenetically featured data that is carried a couple of generations further down the cellular level.

Epigenetic information is not stored within nucleotide sequences but in the chemical modifications of these sequences (like the methylation of repeated strings of GC dinucleotide). Third is the storage of data generated as a result of dynamic interactions between proteins, RNA and DNA in order to adapt to the events and changes during cellular life cycle in the form of nucleoprotein or DNA-protein complexes.

The data generation and storage capacity of DNA in three different hierarchical levels and time periods demonstrates that genome plays a plethora of roles in cellular activities and heredity. Formatting of genome for its generation and storage of data is carried out via DNA sequences of various features. Genomic system is composed of repeating DNA sequences. DNA sequences (satellite) function as a marker as they repeat numerous times in various frequencies.

Genome includes genomic folders similar to that of computer systems. These genomic folders, also known as the epigenetic index of genomes, are responsible for the remodeling of chromatin and the coordinated control of genomic functions. Repeating DNA sequences play a critical role in replication of genome (making a copy of DNA), dispersal of copied DNA into daughter cells and construction of support systems that enable organization of chromatins.

It is possible to better understand genomic functions in relation to examples such as memory sticks and hard drives that are used in electronic information systems. The difference between a genome as a basic data-information storage medium from a hard disc is that it can be replicated as required by its nature and these replicas can be transferred to daughter cells.

Following examples could be given to illustrate that a genome gains function only when it interacts with various data processing modules in the cell.

a) A copy of genome is produced by cellular DNA replication system.

b) Correct localization of each genome copy towards daughter cells is only possible when chromosome segregation system works (the centrosomes and microtubules).

c) The central transcription system is responsible for the copy of data from DNA to RNA. Different gene expression patterns are developed via regulation of transcription time and level with the help of transcription factors and a web of cell signalization. Very intricately organized genomic system structures are designed through the successive combination of protein encoding sequences, signals distributed in various places and repeating DNA sequences. Formatting of genome resembles formatting of computer programs.

Genetic Data & Human Genome Sequence

Various repeated serial commands of computer software are used to allocate addresses to files independent of the original data contained; different computer systems use different signals and structures to manage programs. In a similar fashion, diverse living species often utilize repeating DNA sequences and chromosomal structures to organize the encoded information and to format their genomes.

Diversity and variation of repeating DNA sequences are building blocks that are constructed into different genomic system structures. Genomes of different organisms bear characteristic system morphology just like computers with various operating systems and hardware. For instance, animal cells are created as a good model to take and incorporate foreign DNA into their genomes.

Genetic data transfer among organisms of the same kind is referred to as “vertical gene transfer” whereas transfers between different species, genuses and classes are called “horizontal gene transfer.” Mobile DNA sequences like transposons are very effective horizontal gene transfer agents. Cellular differentiation and morphogenesis (formation of tissue and organ from cell) is not programmed completely in the primary structure of the DNA sequence. Components of modular programs are encoded in a flexible way and a continuous renewed and recombined arrangement is enabled when needed.

The reason behind creation of different organisms from a single genome is this utilization of such genomic structure. Metamorphosis, that is the development of different organisms like invertebrates such as a caterpillar and a butterfly, is a good example of this feature. Two organisms from the perspective of the same genomic protein and RNA codes can be considered as two different species.

Different genomic structures and repetition of sequences among different organisms are distinctive criteria for the identification of species since these features can lead to mismatch of reproductive cells, different expression patterns of genetic code sequences, and may cause ecological diversity as well. That is why repeated DNA sequences are very important in studying parental relationships.

Today, microsatellite DNA as repeated DNA sequences are used to configure biological relations among individuals in forensic sciences. Plant species vary in respect to the repeated sequences in centromeres in their chromosomes; these variations are used for identification of species. Main determinants of genomic system structure are diversity, frequency, and genomic localization of repeated DNA sequences.

To explain this with examples, we could say that successively repeated sequences at centromeres, telomere repetitions and transcription, packing of chromatin, repeated sequences that are spread throughout genome in charge of cellular functions like nucleus localization are the main elements of the genome system structure. Genome is a single integrated system that is controlled closely and remotely via communication webs that use repeated sequences.

While explaining the Qur’anic concept of the Manifest Record (36:12) Bediuzzaman Said Nursi, the great renovator of Islamic thought in Turkey in the twentieth century, wrote that the Manifest Record expresses one aspect of Divine knowledge that is related “more to the past and future than to the present. It is a book of Divine Destiny that contains the origins, roots, and seeds of things, rather than their flourishing forms in their visible existence” (30th Word, Second Aim).

Inspired from this view, a seed can be considered as a tiny adorned form of Divinely creative command as programs and indexes and as a determinant for those programs and indexes in the organization of an entire tree. Since the Manifest Record book, as a title of Divine knowledge and command, observes the past and the future rather than the present, the genome of a grain or a seed acts like a library and an archive in which the future and past of an organism is written.

Sequences Encoding Different Information in DNA

Different information types corresponding with various DNA sequences exist in the genome. These DNA sequences that were considered junk for a long time because they were not coding proteins, have in fact been found to be responsible for an amazing array of functions in genomic structure. Some of these sequences include:

1) Group determining sequences that enable coordinated or successive expression of genes,

2) Sequences acting as a marker in charge of initiation and termination during transcription of DNA to RNA,

3) Signal sequences responsible for conversion of primary immature RNA, sequences into smaller functional RNA molecules,

4) Transcription control sequences that determine the expression frequency of genes,

5) Sequences that identify and mark the initiation regions for intensification and remodeling of chromatins,

6) Sequences that make binding regions which affect the relocation of genome in nucleus or nucleolus,

7) Sequences that target regions where covalent DNA modification (methylation) with functional groups like methyl takes place,

8) Sequences that control and identify the regions responsible for initiation of DNA replication,

9) Sequences that make the structures which enable completion of replication at terminal ends,

10) Sequences at the segregation points that enable equal distribution of copied DNA molecules into daughter cells and centromere sequences,

11) Sequences responsible for guidance during repair of DNA bound errors and damages,

12) Start point sequences used for repackaging of genomes, Recurring sequences exist in the genomes of many organisms and shows great structural diversity. Recurring elements function as an initiator or terminator for heterochromatin regions.

Furthermore they form an important scaffold and binding spots for folding of DNA structure. As if they carry out the job of an architectural mold in specific shaping of genome to be packed into a very limited area.

The ratio of repeating sequences in genome (60-90%) is much more than sequences that are encoding proteins and RNA (10-40%). To explain it with an example, chromosomes in human genome are made up of packages of protein-DNA such as heterochromatin and euchromatin. Heterochromatin regions usually make up the regions with no transcription whereas euchromatin regions feature DNA transcription.

The ratio of protein encoding sequences to the entire human DNA is approximately 1.2%. Around 43% of euchromatin regions are composed of recurring and mobile DNA elements. 18% of heterochromatin region is also made of satellite (dense repeating sequences) and mobile DNA elements. Therefore almost 50% of human genomic DNA is composed of these repeating DNA sequences. In bacteria however, these only make up around 5-10% of the genome.

These sequences were described as parasitic and junk individual DNA structures up until today and still continues to be described thus by many researchers and scientist. Nevertheless, even today, mobile DNA elements and repeating sequences are accepted as genomic parasites. Recent advances in the last ten years that have demonstrated this is not true, have instead revealed the vital importance of repeating sequences in genomic functions.

Repeating DNA sequences affect chromatin (dense pack of DNA and protein) structure in two ways. Irregular repeating DNA sequence copies contain binding regions for proteins that organize DNA. Heterochromatin (darker since it is densely packed chromatin) inhibits transcription and recombination, delays replication, and generally blocks the reading of information in DNA sequences that contain genetic coding.

Heterochromatin regions are distributed throughout the chromosome. Because of this, presence of regions with coupled successive repeated sequences triggers heterochromatin formation. In fruit flies, placement of protein encoding loci required for eye pigmentation near the heterochromatin blocks in centromeres (phenomenon of position effect) is provided via organization of chromosomes and thus, formation of phenotypic characters are inhibited. The “phenomenon of position effect” is convincing evidence that genome is a major system which is integrated with composition of partially repeating DNA sequences.

When heterochromatin amount is increased in XYY male fruit flies, reorganized pigmentation of eye expression decreases. In XO males, when heterochromatin amount decreases, inhibition becomes severe. Changes in levels of protein which binds to special heterochromatin specific DNA regions generate opposite effects. Decrease in these proteins reduces or suppresses “phenomenon of position effect.” Surplus synthesis of these proteins also enriches this effect.

Repeating DNA sequences play an important role in the transfer of genome into daughter cells. For instance, they function in formation of the centromeres as chromosomal binding regions for microtubules, during gamete formation as linear terminals of chromosomes are replicated, and during chromosomal matching. Distribution of repeating sequences plays a major role in configuration of genomic functions. Each genome has genomic system structure that is shaped dependent on the amount of repeating DNA sequences to a major extent.

Going back to Nursi’s explanation of the Manifest Record, we can draw a parallelism between the book of the universe and the book of revelation, the first of which shows us that certain sequences in the genome are repeated for significance and necessity, just as many verses are repeated frequently in the Qur’an with nuances to refer to different meanings, benefits, and purposes, opening a wider space for many interpretations.

A genome is not only a book that contains protein and RNA codes, but also has a complex system structure with many functions for cellular vitality. The most needed sequences are those that are repeated more frequently. They are not pieces of junk DNA as predicted, they are jewels Divinely constructed.

  References

Shapiro J. A. 2001. “Genome Formatting for Computation and Function: Genome Organization and Reorganization in Evolution: Formatting for Computation and Function.” Presented at a symposium on “Contextualizing the Genome,” Ghent University, Belgium, November 25 – 28, 2001 (Ann. N.Y. Acad. Sci., in press).

Shapiro, J.A. 2005. “A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering.” Gene 345, pp: 91–100.

Shapiro J. A. and Sternberg R. V. 2005. “Why repetitive DNA is essential to genome function.” Biol. Rev., 80, pp. 1–24. Cambridge Philosophical Society.

———-

Taken with slight editorial modifications from: Fountain Magazine: Issue 93 / May – June 2013.

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