This book introduces the general reader and the specialist to the new order of things in evolutio... more This book introduces the general reader and the specialist to the new order of things in evolution , the origin of life on Earth , and the question of life on Mars and Europa and elsewhere in the universe. Although there are many fields of biology that are essentially descriptive , with the application of in formation theory , theoretical biology can now take its place with theoretical physics without apology. Thus biology has become a quantitative and com putational science as George Gamow (1904-68) suggested. By employing information theory , comparisons between the genetics of organisms can now be made quantitatively with the same accuracy that is typical of astronomy , physics , and chemistry. Spacecraft send messages to Earth as they pass the outer planets-Mars , Jupiter , Saturn , Uranus , Neptune , and Pluto-in spite of the small amount of energy available. Enormous amounts of data and information flow about on the Internet. Huge sums of money are transferred every day. Errors in these communications cannot be tolerated. Claude Shannon (1916-200 1) showed that this is accomplished because communication is segregated, linear, and digital so that sufficient redundance can be introduced in communication codes to overcome errors. Furthermore , he showed that these signals , which contain messages , can be measured in bits and bytes, terms that are familiar to computer users. Watson and Crick discovered that there is a genetic message , recorded in the digital sequence of nucleotides in DNA, that controls the formation of protein and of course all biological processes. The message in the genetic information system is segregated, linear, and digital and can be measured in bits and bytes. Computer users will notice the isomorphism between the lX Preface Xl DNA now plays a role in forensics identi fication that is far more im portant than fingerprints. Forensics has reached new levels of certainty. A number of guilty people have been convicted, and others , falsely accused by conventional methods , have been vindicated. This is a monograph and not an encyclopedia so I have not considered it necessary to call attention to papers I believe did not make an important contribution or those which are incorrect. I have included in the references only those I felt contributed to the point I was making. Some readers may think that I have neglected an important paper here and there. I acknowledge that this may be the case , but there are times when one must hew to the line and let the chips fall where they may. This monograph follows my interest in the sub ject , which was first at tracted by the work of Dr. Henry Quastler (1908-63). With his collaboration I organized the Symposium on Information Theory in Biology at Gatlinburg , Te nnessee , in October 1956. I am indebted to the late Professor Thomas Hughes Jukes (1906-99) , whose strong recommendations resulted in my original papers being published. Many of Professor Jukes' important con tributions to molecular biology have shaped the ideas presented in this book , particularly those concerning the evolution of the genetic code. I am grateful to Dr. Gregory J. Chaitin , whose original and seminal work in algorithmic information theory is reflected throughout the book .
The freshwater walking catfish Clarias magur (Hamilton, 1822) is one of the most popular aquacult... more The freshwater walking catfish Clarias magur (Hamilton, 1822) is one of the most popular aquaculture fishes in Indian and the Asian subcontinent because of its nutritional value and great taste. Muscle proteome of C. magur was studied. Muscle tissue is of significance in fishes due to presence of high protein content and poly unsaturated fatty acids (PUFA) proved to have medicinal and therapeutic value. Fishes procured were acclimatised and muscle tissue was studied. Briefly, muscle protein extract prepared from C. magur, by homogenizing muscle tissue in 50 mMTris buffer with protease inhibitor for downstream processing, digested with trypsin in solution, reduced with dithiothreitol (DTT) and alkylated with iodoacetamide (IAA) for LC/MS analysis. The peptides were separated on Waters Synapt G2 Q-TOF equipped with Electro-Spray ionisation (ESI) for DATA independent acquisition for MS analysis. The raw data was processed by Protein Lynx Global Server (PLGS) software. Peptide tolerance limit was set at 50 ppm with minimum fragment match of 2 peptides for proteins. In silico approach was used to retrieve ACPs from muscle proteome derived from LC/MS by BIOPEP, Anti-CP and iDACP online servers. Out of a total of 468 peptides, 60 peptides showed anti-cancer peptide (ACPs) activity. Out of 19 non-allergenic peptides as analysed by AlerPred software, one peptide was toxic as revealed by ToxinPred software. The peptides were ranked with 0.9884 being highest and 0.0341 being the lowest by Peptide Ranker tool. This study reports C. magur derived anti-cancer bioactive peptides as a natural, less toxic anti-cancer therapeutic source exhibiting anti-cancer activity by activating apoptosis in mitochondria slaying cancer cells.
The CRISPR/Cas9 system is a genome-editing tool that allows for precise and efficient modificatio... more The CRISPR/Cas9 system is a genome-editing tool that allows for precise and efficient modifications to the DNA of a cell. This technology can be used in endophytic fungi, which live within plants and can have beneficial effects on their host, making them important for agriculture. Using CRISPR/Cas9, researchers can introduce specific genetic changes into endophytic fungal genomes, allowing them to study the function of genes, improve their plant-growth-promoting properties, and create new, more beneficial endophytes. This system works by using the Cas9 protein, which acts as a pair of molecular scissors, to cut DNA at specific locations determined by a guide RNA. Once the DNA is cut, the cell’s natural repair mechanisms can be used to insert or delete specific genes, allowing for precise editing of the fungal genome. This article discusses the mechanism and applications of CRISPR/Cas9 to fungal endophytes.
Retinoids play an important role in development, differentiation, and homeostasis. The discovery ... more Retinoids play an important role in development, differentiation, and homeostasis. The discovery of retinoid receptors belonging to the superfamily of nuclear ligand-activated transcriptional regulators has revolutionized our molecular understanding as to how these structurally simple molecules exert their pieiotropic effects. Diversity in the control of gene expression by retinoid signals is generated through complexity at different levels of the signaling pathway. A major source of diversity originates from the existence of two families of retinoid acid (RA) receptors (R), the RAR isotypes (a, f, and 'y) and the three RXR isotypes (a, 3, and 'y), and their numerous isoforms, which bind as RXR/RAR heterodimers to the polymorphic cis-acting response elements of RA target genes. The possibility of cross-modulation (cross-talk) with cell-surface receptors signaling pathways, as well as the finding that RAils and RXRs interact with multipie putative coactivators and/or corepressors, generates additional levels of complexity for the array of combinatorial effects that underlie the pieiotropic effects of retinoids. This review focuses on recent developments, particularly in the area of structurefunction reiationships.-Chamhon, P. A decade of molecular biology of retinoic acid receptors.
The major type of receptor for the inhibitory neurotransmitter γ‐aminobutyric acid (GABA), called... more The major type of receptor for the inhibitory neurotransmitter γ‐aminobutyric acid (GABA), called the GABAA receptor, is a member of a gene superfamily of ligand‐gated ion channels. This receptor is a heterooligomeric protein composed of several distinct polypeptide types (α, β, γ, and δ). Molecular cloning of these polypeptides reveals that they show 20‐40% identity with each other, and 10‐20% identity with polypeptides of the nicotinic acetylcholine receptors and strychnine‐sensitive glycine receptor. Each polypeptide type is also represented by a family of genes whose members have 60‐80% amino acid sequence identity. Regions of conserved and variable amino acid sequence suggest structural and functional domains within each polypeptide. All of the polypeptides when expressed in heterologous cells produce GABA‐activated chloride channels, and the different subtypes express different pharmacological properties. The distributions of mRNAs for the different GABAA receptor polypeptides and their subtypes show significant brain regional variation consistent with pharmacological and biochemical evidence for receptor heterogeneity. Subpopulations of GABAA receptors with different cellular and regional locations show differential sensitivity to GABA, to modulators like steroids, to physiological regulation, to disease processes, and to pharmacological manipulation by drugs such as benzodiazepines. The properties of the different subpopulations of GABAA receptors are determined by which one or more of the different polypeptides and their subtypes are expressed in a given cell to produce a variety of different oligomeric protein structures. Molecular cloning techniques have produced rapid advances in understanding the GABAA receptor protein family.— Olsen, R. W.; Tobin, A. J. Molecular biology of GABAA receptors. FASEB J. 4: 1469‐1480; 1990.
Shafii B and Price WJ, 1998. Analysis of genotype-byenvironment interaction using the additive ma... more Shafii B and Price WJ, 1998. Analysis of genotype-byenvironment interaction using the additive main effects and multiplicative interaction model and stability estimates.
The application of modern molecular biological methods has had an increasing and dramatic impact ... more The application of modern molecular biological methods has had an increasing and dramatic impact upon the discipline of molecular neuropharmacology. This is particularly true for the study of neurotransmitter receptors, where the use of recombinant DNA techniques has resulted in the cloning of multiple and sometimes unexpected receptor subtypes for a given neurotransmitter and, in some cases, the cloning of receptors for which no neurotransmitter is known. Within the past couple of years, it has become readily apparent that dopamine receptors will be no exception to this trend. Five different dopamine receptors have now been cloned and identified using molecular biological techniques, while only a few years ago only two receptor subtypes were thought to exist. David Sibley and Frederick Monsma review the molecular characteristics of the recently cloned dopamine receptors and discuss prospects for the cloning and identification of additional subtypes in this receptor family.
Until recently, it has been impossible to approach learning with the techniques of cell biology. ... more Until recently, it has been impossible to approach learning with the techniques of cell biology. During the past several years, elementary forms of learning have been analyzed in higher invertebrates. Their nervous systems allow the experimental study of behavioral, neurophysiological, morphological, biochemical, and genetic components of the functional (plastic) changes underlying learning. In this review, we focus primarily on short-term sensitization of the gill and siphon reflex in the marine mollusk, Aplysia californica. Analyses of this form of learning provide direct evidence that protein phosphorylation dependent on cyclic adenosine monophosphate can modulate synaptic action. These studies also suggest how the molecular mechanisms for this short-term form of synaptic plasticity can be extended to explain both long-term memory and classical conditioning.
Proceedings of the National Academy of Sciences, 1996
All multicellular organisms have mechanisms for killing their own cells, and use physiological ce... more All multicellular organisms have mechanisms for killing their own cells, and use physiological cell death for defence, development, homeostasis, and aging. Apoptosis is a morphologically recognizable form of cell death that is implemented by a mechanism that has been conserved throughout evolution from nematode to man. Thus homologs of the genes that implement cell death in nematodes also do so in mammals, but in mammals the process is considerably more complex, involving multiple isoforms of the components of the cell death machinery. In some circumstances this allows independent regulation of pathways that converge upon a common end point. A molecular understanding of this mechanism may allow design of therapies that either enhance or block cell death at will.
of a very exciting and intensive meeting that took place on September 12-14, 1996, at the EMBL in... more of a very exciting and intensive meeting that took place on September 12-14, 1996, at the EMBL in Heidelberg. Instituto Cajal, CSIC 28002 Madrid The workshop, entitled "Molecular Biology of Axon Guidance," gathered a forum of 26 speakers and some Spain 90 people in total, who enthusiastically presented and discussed the recent advances in the field. I will summarize the meeting in this review, emphasizing some of the More than a century ago, Cajal published one of his new data presented. most significant contributions, the discovery of the The topics of the meeting were quite varied but many growth cone as the terminal structure of the developing of the speakers concentrated on axonal guidance in the neuronal cell. This finding was a crucial step in the estabtwo models used to describe the growth cone and the lishment of the theory that neurons develop as individual chemoaffinity theory, namely the midline and the retinocells. tectal system; the starring molecules were members of ".. This fibre [of the commissural neuron] ends...in an the collapsin/semaphorin family, the netrins, and the enlargement which may be rounded and subtle, but that Eph-related receptor family and their ligands. may also adopt a conical appearance. This latter we shall name the growth cone, that at times displays fine The Eph-Related Receptor Family and short extensions...which appear to insinuate themand Their Ligands selves between the surrounding elements, relentlessly Receptor tyrosine kinases (RTKs) have been subdivided forging a path through the interstitial matrix" (Ramó n y into 14 different families according to sequence similar-Cajal, 1890a, Figure 1). ity, mainly based on their extracellular domains. Over the past five years, the Eph family of receptors (named Apart from a very precise definition of the growth cone, one can also find in Cajal's writings the origin of for the first member of the family; Hirai et al., 1987) has attracted a lot of attention from people working on axon the neurotropic theory and of the mechanism of axonal pathfinding. Two years later, after the analysis of the pathfinding. Although this family had been thought to be excellent candidates to play important roles in the developing retinotectal connections, and by extrapolation from Pfeffer's chemotaxis theory, Cajal proposed development of the vertebrate embryo, until recently they were were referred to as "orphan receptors" be-that developing neurons possessed chemotactic properties that would guide axons to their targets. He sug-cause of the absence of known ligands that could bind to them. Today, the Eph family is the largest subfamily gested that the growth cone would be guided by "chemical flows" that they would follow to find the secretory of RTKs, comprising at least 14 members. These bind to a novel family of ligands with eight members already target (Ramó n y Cajal, 1893). This suggestion was neglected for many years in favor of the mechanical theory, described and are considered essential players in many different processes during embryonic development, in-but was brought to light again in the 1940s. Sperry carried out a long series of experimental manipulations cluding the development of the vertebrate nervous system. in the newt that led him to suggest the existence of complementary and recognizable cytochemical tags What are the characteristics of the Eph receptor family? The extracellular region of the receptors contains present in the retina and its target, the optic tectum. Twenty years later, he formulated the chemoaffinity the-an immunoglobulin-like domain, a Cys-rich domain and two fibronectin type III domains, and the cytoplasmic ory in which he postulated the existence of at least two cytochemical gradients superimposed both in the retina region, a single kinase catalytic domain. Different members of the family have been cloned in many vertebrates and the tectum that would provide each axon with a particular target "latitude and longitude," allowing the species, and the sequence similarity among the orthologs is extremely high. The cloning of the first ligand formation of a precise topographic map (Sperry, 1963). We now know that Sperry was partly correct in saying for this receptor family was the result of a very difficult hunting task, looking for receptor binding activity in con-that topographic maps are generated by the existence of chemoaffinity labels, but also that the ultimate refine-ditioned media obtained from more than a hundred cell lines (Bartley et al., 1994). From then on, and at an im-ment of these maps depends on neuronal activity and trophic support. In any case, the growth cones encoun-pressive rate, the identification of seven more ligands has been reported to date. One very important character a great variety of guiding signals, either attractive or repellent that, in addition, can be diffusible or attached teristic of these ligands is that they are all membraneattached proteins, either by a glycophosphotidylinositol to the cell membrane or to the extracellular matrix. We have had to wait until recently to learn the identity of (GPI) linkage or through a transmembrane (TM) domain. Therefore, whenever we talk about any Eph receptor-the actual molecules that do the job. The amount of information accumulated in the last few years through ligand interactions, we are talking about contact-dependent cell to cell communication, as the ligands require the cloning and functional analysis of some of these molecules precipitated the organization by Rudiger membrane attachment (or artificial clustering) for activity (Davis et al., 1994). This fact confers on them unique Klein (European Molecular Biology Laboratory [EMBL], Germany) and John Flanagan (Harvard Medical School) properties that suggest that the cellular responses to
We announce the release of the fourth version of MEGA software, which expands on the existing fac... more We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multiuser supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at http://www.megasoftware.net.
Due to constant health awareness and readily available information on usefulness of different die... more Due to constant health awareness and readily available information on usefulness of different diet and their direct link with health, the demand of functional food is increasing day by day. The concept of functional foods includes foods or food ingredients that exert a beneficial effect on host health and/or reduce the risk of chronic disease beyond basic nutritional functions. Increasing awareness of consumer health and interest in functional foods to achieve a healthy lifestyle has resulted in the need for food products with versatile health-benefiting properties. Cereal-and cereal component-based food products offer opportunities to include probiotics, prebiotics, and fibers in the human diet. Various growth studies using probiotic Lactic acid bacteria on cereal-based substrates and utilization of whole grain or components as high-fiber foods in developing novel food products lend support to the idea that cereal-based media may well be good probiotic carriers. It is essential that science and traditional knowledge should go together to find mutually beneficial results. In the Indian subcontinent, making use of fermented food and beverages using local food crops and other biological resources are very common. But the nature of the products and the base material vary from region to region.
... Special Article. You have full text access to this OnlineOpen article Molecular biology of th... more ... Special Article. You have full text access to this OnlineOpen article Molecular biology of the hepatitis C viruses: Implications for diagnosis, development and control of viral disease. Michael Houghton Ph.D.,; Amy Weiner,; Jang Han,; George Kuo,; Qui-Lim Choo. ...
This book introduces the general reader and the specialist to the new order of things in evolutio... more This book introduces the general reader and the specialist to the new order of things in evolution , the origin of life on Earth , and the question of life on Mars and Europa and elsewhere in the universe. Although there are many fields of biology that are essentially descriptive , with the application of in formation theory , theoretical biology can now take its place with theoretical physics without apology. Thus biology has become a quantitative and com putational science as George Gamow (1904-68) suggested. By employing information theory , comparisons between the genetics of organisms can now be made quantitatively with the same accuracy that is typical of astronomy , physics , and chemistry. Spacecraft send messages to Earth as they pass the outer planets-Mars , Jupiter , Saturn , Uranus , Neptune , and Pluto-in spite of the small amount of energy available. Enormous amounts of data and information flow about on the Internet. Huge sums of money are transferred every day. Errors in these communications cannot be tolerated. Claude Shannon (1916-200 1) showed that this is accomplished because communication is segregated, linear, and digital so that sufficient redundance can be introduced in communication codes to overcome errors. Furthermore , he showed that these signals , which contain messages , can be measured in bits and bytes, terms that are familiar to computer users. Watson and Crick discovered that there is a genetic message , recorded in the digital sequence of nucleotides in DNA, that controls the formation of protein and of course all biological processes. The message in the genetic information system is segregated, linear, and digital and can be measured in bits and bytes. Computer users will notice the isomorphism between the lX Preface Xl DNA now plays a role in forensics identi fication that is far more im portant than fingerprints. Forensics has reached new levels of certainty. A number of guilty people have been convicted, and others , falsely accused by conventional methods , have been vindicated. This is a monograph and not an encyclopedia so I have not considered it necessary to call attention to papers I believe did not make an important contribution or those which are incorrect. I have included in the references only those I felt contributed to the point I was making. Some readers may think that I have neglected an important paper here and there. I acknowledge that this may be the case , but there are times when one must hew to the line and let the chips fall where they may. This monograph follows my interest in the sub ject , which was first at tracted by the work of Dr. Henry Quastler (1908-63). With his collaboration I organized the Symposium on Information Theory in Biology at Gatlinburg , Te nnessee , in October 1956. I am indebted to the late Professor Thomas Hughes Jukes (1906-99) , whose strong recommendations resulted in my original papers being published. Many of Professor Jukes' important con tributions to molecular biology have shaped the ideas presented in this book , particularly those concerning the evolution of the genetic code. I am grateful to Dr. Gregory J. Chaitin , whose original and seminal work in algorithmic information theory is reflected throughout the book .
The freshwater walking catfish Clarias magur (Hamilton, 1822) is one of the most popular aquacult... more The freshwater walking catfish Clarias magur (Hamilton, 1822) is one of the most popular aquaculture fishes in Indian and the Asian subcontinent because of its nutritional value and great taste. Muscle proteome of C. magur was studied. Muscle tissue is of significance in fishes due to presence of high protein content and poly unsaturated fatty acids (PUFA) proved to have medicinal and therapeutic value. Fishes procured were acclimatised and muscle tissue was studied. Briefly, muscle protein extract prepared from C. magur, by homogenizing muscle tissue in 50 mMTris buffer with protease inhibitor for downstream processing, digested with trypsin in solution, reduced with dithiothreitol (DTT) and alkylated with iodoacetamide (IAA) for LC/MS analysis. The peptides were separated on Waters Synapt G2 Q-TOF equipped with Electro-Spray ionisation (ESI) for DATA independent acquisition for MS analysis. The raw data was processed by Protein Lynx Global Server (PLGS) software. Peptide tolerance limit was set at 50 ppm with minimum fragment match of 2 peptides for proteins. In silico approach was used to retrieve ACPs from muscle proteome derived from LC/MS by BIOPEP, Anti-CP and iDACP online servers. Out of a total of 468 peptides, 60 peptides showed anti-cancer peptide (ACPs) activity. Out of 19 non-allergenic peptides as analysed by AlerPred software, one peptide was toxic as revealed by ToxinPred software. The peptides were ranked with 0.9884 being highest and 0.0341 being the lowest by Peptide Ranker tool. This study reports C. magur derived anti-cancer bioactive peptides as a natural, less toxic anti-cancer therapeutic source exhibiting anti-cancer activity by activating apoptosis in mitochondria slaying cancer cells.
The CRISPR/Cas9 system is a genome-editing tool that allows for precise and efficient modificatio... more The CRISPR/Cas9 system is a genome-editing tool that allows for precise and efficient modifications to the DNA of a cell. This technology can be used in endophytic fungi, which live within plants and can have beneficial effects on their host, making them important for agriculture. Using CRISPR/Cas9, researchers can introduce specific genetic changes into endophytic fungal genomes, allowing them to study the function of genes, improve their plant-growth-promoting properties, and create new, more beneficial endophytes. This system works by using the Cas9 protein, which acts as a pair of molecular scissors, to cut DNA at specific locations determined by a guide RNA. Once the DNA is cut, the cell’s natural repair mechanisms can be used to insert or delete specific genes, allowing for precise editing of the fungal genome. This article discusses the mechanism and applications of CRISPR/Cas9 to fungal endophytes.
Retinoids play an important role in development, differentiation, and homeostasis. The discovery ... more Retinoids play an important role in development, differentiation, and homeostasis. The discovery of retinoid receptors belonging to the superfamily of nuclear ligand-activated transcriptional regulators has revolutionized our molecular understanding as to how these structurally simple molecules exert their pieiotropic effects. Diversity in the control of gene expression by retinoid signals is generated through complexity at different levels of the signaling pathway. A major source of diversity originates from the existence of two families of retinoid acid (RA) receptors (R), the RAR isotypes (a, f, and 'y) and the three RXR isotypes (a, 3, and 'y), and their numerous isoforms, which bind as RXR/RAR heterodimers to the polymorphic cis-acting response elements of RA target genes. The possibility of cross-modulation (cross-talk) with cell-surface receptors signaling pathways, as well as the finding that RAils and RXRs interact with multipie putative coactivators and/or corepressors, generates additional levels of complexity for the array of combinatorial effects that underlie the pieiotropic effects of retinoids. This review focuses on recent developments, particularly in the area of structurefunction reiationships.-Chamhon, P. A decade of molecular biology of retinoic acid receptors.
The major type of receptor for the inhibitory neurotransmitter γ‐aminobutyric acid (GABA), called... more The major type of receptor for the inhibitory neurotransmitter γ‐aminobutyric acid (GABA), called the GABAA receptor, is a member of a gene superfamily of ligand‐gated ion channels. This receptor is a heterooligomeric protein composed of several distinct polypeptide types (α, β, γ, and δ). Molecular cloning of these polypeptides reveals that they show 20‐40% identity with each other, and 10‐20% identity with polypeptides of the nicotinic acetylcholine receptors and strychnine‐sensitive glycine receptor. Each polypeptide type is also represented by a family of genes whose members have 60‐80% amino acid sequence identity. Regions of conserved and variable amino acid sequence suggest structural and functional domains within each polypeptide. All of the polypeptides when expressed in heterologous cells produce GABA‐activated chloride channels, and the different subtypes express different pharmacological properties. The distributions of mRNAs for the different GABAA receptor polypeptides and their subtypes show significant brain regional variation consistent with pharmacological and biochemical evidence for receptor heterogeneity. Subpopulations of GABAA receptors with different cellular and regional locations show differential sensitivity to GABA, to modulators like steroids, to physiological regulation, to disease processes, and to pharmacological manipulation by drugs such as benzodiazepines. The properties of the different subpopulations of GABAA receptors are determined by which one or more of the different polypeptides and their subtypes are expressed in a given cell to produce a variety of different oligomeric protein structures. Molecular cloning techniques have produced rapid advances in understanding the GABAA receptor protein family.— Olsen, R. W.; Tobin, A. J. Molecular biology of GABAA receptors. FASEB J. 4: 1469‐1480; 1990.
Shafii B and Price WJ, 1998. Analysis of genotype-byenvironment interaction using the additive ma... more Shafii B and Price WJ, 1998. Analysis of genotype-byenvironment interaction using the additive main effects and multiplicative interaction model and stability estimates.
The application of modern molecular biological methods has had an increasing and dramatic impact ... more The application of modern molecular biological methods has had an increasing and dramatic impact upon the discipline of molecular neuropharmacology. This is particularly true for the study of neurotransmitter receptors, where the use of recombinant DNA techniques has resulted in the cloning of multiple and sometimes unexpected receptor subtypes for a given neurotransmitter and, in some cases, the cloning of receptors for which no neurotransmitter is known. Within the past couple of years, it has become readily apparent that dopamine receptors will be no exception to this trend. Five different dopamine receptors have now been cloned and identified using molecular biological techniques, while only a few years ago only two receptor subtypes were thought to exist. David Sibley and Frederick Monsma review the molecular characteristics of the recently cloned dopamine receptors and discuss prospects for the cloning and identification of additional subtypes in this receptor family.
Until recently, it has been impossible to approach learning with the techniques of cell biology. ... more Until recently, it has been impossible to approach learning with the techniques of cell biology. During the past several years, elementary forms of learning have been analyzed in higher invertebrates. Their nervous systems allow the experimental study of behavioral, neurophysiological, morphological, biochemical, and genetic components of the functional (plastic) changes underlying learning. In this review, we focus primarily on short-term sensitization of the gill and siphon reflex in the marine mollusk, Aplysia californica. Analyses of this form of learning provide direct evidence that protein phosphorylation dependent on cyclic adenosine monophosphate can modulate synaptic action. These studies also suggest how the molecular mechanisms for this short-term form of synaptic plasticity can be extended to explain both long-term memory and classical conditioning.
Proceedings of the National Academy of Sciences, 1996
All multicellular organisms have mechanisms for killing their own cells, and use physiological ce... more All multicellular organisms have mechanisms for killing their own cells, and use physiological cell death for defence, development, homeostasis, and aging. Apoptosis is a morphologically recognizable form of cell death that is implemented by a mechanism that has been conserved throughout evolution from nematode to man. Thus homologs of the genes that implement cell death in nematodes also do so in mammals, but in mammals the process is considerably more complex, involving multiple isoforms of the components of the cell death machinery. In some circumstances this allows independent regulation of pathways that converge upon a common end point. A molecular understanding of this mechanism may allow design of therapies that either enhance or block cell death at will.
of a very exciting and intensive meeting that took place on September 12-14, 1996, at the EMBL in... more of a very exciting and intensive meeting that took place on September 12-14, 1996, at the EMBL in Heidelberg. Instituto Cajal, CSIC 28002 Madrid The workshop, entitled "Molecular Biology of Axon Guidance," gathered a forum of 26 speakers and some Spain 90 people in total, who enthusiastically presented and discussed the recent advances in the field. I will summarize the meeting in this review, emphasizing some of the More than a century ago, Cajal published one of his new data presented. most significant contributions, the discovery of the The topics of the meeting were quite varied but many growth cone as the terminal structure of the developing of the speakers concentrated on axonal guidance in the neuronal cell. This finding was a crucial step in the estabtwo models used to describe the growth cone and the lishment of the theory that neurons develop as individual chemoaffinity theory, namely the midline and the retinocells. tectal system; the starring molecules were members of ".. This fibre [of the commissural neuron] ends...in an the collapsin/semaphorin family, the netrins, and the enlargement which may be rounded and subtle, but that Eph-related receptor family and their ligands. may also adopt a conical appearance. This latter we shall name the growth cone, that at times displays fine The Eph-Related Receptor Family and short extensions...which appear to insinuate themand Their Ligands selves between the surrounding elements, relentlessly Receptor tyrosine kinases (RTKs) have been subdivided forging a path through the interstitial matrix" (Ramó n y into 14 different families according to sequence similar-Cajal, 1890a, Figure 1). ity, mainly based on their extracellular domains. Over the past five years, the Eph family of receptors (named Apart from a very precise definition of the growth cone, one can also find in Cajal's writings the origin of for the first member of the family; Hirai et al., 1987) has attracted a lot of attention from people working on axon the neurotropic theory and of the mechanism of axonal pathfinding. Two years later, after the analysis of the pathfinding. Although this family had been thought to be excellent candidates to play important roles in the developing retinotectal connections, and by extrapolation from Pfeffer's chemotaxis theory, Cajal proposed development of the vertebrate embryo, until recently they were were referred to as "orphan receptors" be-that developing neurons possessed chemotactic properties that would guide axons to their targets. He sug-cause of the absence of known ligands that could bind to them. Today, the Eph family is the largest subfamily gested that the growth cone would be guided by "chemical flows" that they would follow to find the secretory of RTKs, comprising at least 14 members. These bind to a novel family of ligands with eight members already target (Ramó n y Cajal, 1893). This suggestion was neglected for many years in favor of the mechanical theory, described and are considered essential players in many different processes during embryonic development, in-but was brought to light again in the 1940s. Sperry carried out a long series of experimental manipulations cluding the development of the vertebrate nervous system. in the newt that led him to suggest the existence of complementary and recognizable cytochemical tags What are the characteristics of the Eph receptor family? The extracellular region of the receptors contains present in the retina and its target, the optic tectum. Twenty years later, he formulated the chemoaffinity the-an immunoglobulin-like domain, a Cys-rich domain and two fibronectin type III domains, and the cytoplasmic ory in which he postulated the existence of at least two cytochemical gradients superimposed both in the retina region, a single kinase catalytic domain. Different members of the family have been cloned in many vertebrates and the tectum that would provide each axon with a particular target "latitude and longitude," allowing the species, and the sequence similarity among the orthologs is extremely high. The cloning of the first ligand formation of a precise topographic map (Sperry, 1963). We now know that Sperry was partly correct in saying for this receptor family was the result of a very difficult hunting task, looking for receptor binding activity in con-that topographic maps are generated by the existence of chemoaffinity labels, but also that the ultimate refine-ditioned media obtained from more than a hundred cell lines (Bartley et al., 1994). From then on, and at an im-ment of these maps depends on neuronal activity and trophic support. In any case, the growth cones encoun-pressive rate, the identification of seven more ligands has been reported to date. One very important character a great variety of guiding signals, either attractive or repellent that, in addition, can be diffusible or attached teristic of these ligands is that they are all membraneattached proteins, either by a glycophosphotidylinositol to the cell membrane or to the extracellular matrix. We have had to wait until recently to learn the identity of (GPI) linkage or through a transmembrane (TM) domain. Therefore, whenever we talk about any Eph receptor-the actual molecules that do the job. The amount of information accumulated in the last few years through ligand interactions, we are talking about contact-dependent cell to cell communication, as the ligands require the cloning and functional analysis of some of these molecules precipitated the organization by Rudiger membrane attachment (or artificial clustering) for activity (Davis et al., 1994). This fact confers on them unique Klein (European Molecular Biology Laboratory [EMBL], Germany) and John Flanagan (Harvard Medical School) properties that suggest that the cellular responses to
We announce the release of the fourth version of MEGA software, which expands on the existing fac... more We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multiuser supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at http://www.megasoftware.net.
Due to constant health awareness and readily available information on usefulness of different die... more Due to constant health awareness and readily available information on usefulness of different diet and their direct link with health, the demand of functional food is increasing day by day. The concept of functional foods includes foods or food ingredients that exert a beneficial effect on host health and/or reduce the risk of chronic disease beyond basic nutritional functions. Increasing awareness of consumer health and interest in functional foods to achieve a healthy lifestyle has resulted in the need for food products with versatile health-benefiting properties. Cereal-and cereal component-based food products offer opportunities to include probiotics, prebiotics, and fibers in the human diet. Various growth studies using probiotic Lactic acid bacteria on cereal-based substrates and utilization of whole grain or components as high-fiber foods in developing novel food products lend support to the idea that cereal-based media may well be good probiotic carriers. It is essential that science and traditional knowledge should go together to find mutually beneficial results. In the Indian subcontinent, making use of fermented food and beverages using local food crops and other biological resources are very common. But the nature of the products and the base material vary from region to region.
... Special Article. You have full text access to this OnlineOpen article Molecular biology of th... more ... Special Article. You have full text access to this OnlineOpen article Molecular biology of the hepatitis C viruses: Implications for diagnosis, development and control of viral disease. Michael Houghton Ph.D.,; Amy Weiner,; Jang Han,; George Kuo,; Qui-Lim Choo. ...
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Papers by arpita batta
Indian and the Asian subcontinent because of its nutritional value and great taste. Muscle proteome of C. magur
was studied. Muscle tissue is of significance in fishes due to presence of high protein content and poly unsaturated
fatty acids (PUFA) proved to have medicinal and therapeutic value. Fishes procured were acclimatised and muscle
tissue was studied. Briefly, muscle protein extract prepared from C. magur, by homogenizing muscle tissue in 50
mMTris buffer with protease inhibitor for downstream processing, digested with trypsin in solution, reduced with
dithiothreitol (DTT) and alkylated with iodoacetamide (IAA) for LC/MS analysis. The peptides were separated
on Waters Synapt G2 Q-TOF equipped with Electro-Spray ionisation (ESI) for DATA independent acquisition for
MS analysis. The raw data was processed by Protein Lynx Global Server (PLGS) software. Peptide tolerance limit
was set at 50 ppm with minimum fragment match of 2 peptides for proteins. In silico approach was used to
retrieve ACPs from muscle proteome derived from LC/MS by BIOPEP, Anti-CP and iDACP online servers. Out of a
total of 468 peptides, 60 peptides showed anti-cancer peptide (ACPs) activity. Out of 19 non-allergenic peptides
as analysed by AlerPred software, one peptide was toxic as revealed by ToxinPred software. The peptides were
ranked with 0.9884 being highest and 0.0341 being the lowest by Peptide Ranker tool. This study reports C.
magur derived anti-cancer bioactive peptides as a natural, less toxic anti-cancer therapeutic source exhibiting
anti-cancer activity by activating apoptosis in mitochondria slaying cancer cells.
Indian and the Asian subcontinent because of its nutritional value and great taste. Muscle proteome of C. magur
was studied. Muscle tissue is of significance in fishes due to presence of high protein content and poly unsaturated
fatty acids (PUFA) proved to have medicinal and therapeutic value. Fishes procured were acclimatised and muscle
tissue was studied. Briefly, muscle protein extract prepared from C. magur, by homogenizing muscle tissue in 50
mMTris buffer with protease inhibitor for downstream processing, digested with trypsin in solution, reduced with
dithiothreitol (DTT) and alkylated with iodoacetamide (IAA) for LC/MS analysis. The peptides were separated
on Waters Synapt G2 Q-TOF equipped with Electro-Spray ionisation (ESI) for DATA independent acquisition for
MS analysis. The raw data was processed by Protein Lynx Global Server (PLGS) software. Peptide tolerance limit
was set at 50 ppm with minimum fragment match of 2 peptides for proteins. In silico approach was used to
retrieve ACPs from muscle proteome derived from LC/MS by BIOPEP, Anti-CP and iDACP online servers. Out of a
total of 468 peptides, 60 peptides showed anti-cancer peptide (ACPs) activity. Out of 19 non-allergenic peptides
as analysed by AlerPred software, one peptide was toxic as revealed by ToxinPred software. The peptides were
ranked with 0.9884 being highest and 0.0341 being the lowest by Peptide Ranker tool. This study reports C.
magur derived anti-cancer bioactive peptides as a natural, less toxic anti-cancer therapeutic source exhibiting
anti-cancer activity by activating apoptosis in mitochondria slaying cancer cells.