Gene regulation is vital for life and it involves plethora of mechanisms, including microRNA (miR... more Gene regulation is vital for life and it involves plethora of mechanisms, including microRNA (miRNA) based RNA inhibition. Messenger RNA (mRNA) inhibition by miRNA requires less sequence specificity than inhibition by small inhibitory RNA (siRNA) and has different set of enzymes required for processing. The regulation and richness of RNA inhibition and specifically miRNA action is just beginning to be studied, while much work has undergone in the study of synthesis and processing of miRNA. More than 1800 unique human miRNAs have been computationally predicted and several have been experimentally validated. Given their ability to act as sequence specific regulators of the transcriptome, miRNAs have potential in therapeutics and diagnostics. We specifically focus on synthesis of current therapeutic applications of miRNA. We discuss the two different strategies in miRNA treatment: mimics and antagonists, and bring forward the promises and perils of miRNA therapy in its journey from lab to medicine.
Electric fences have been used more successfully than non-electric fences in comparable settings ... more Electric fences have been used more successfully than non-electric fences in comparable settings for a variety of animals. The frequent breaking of electric fences by large mammals such as elephants that can pull a tree down on the fence, or rhinos that can run through fences with impunity, decrease the effectiveness of electric fences. Laying out a depressed region near the fence with the width more than the tallest tree, and filling it with sand would increase the effectiveness of electric fences. This would force the animal to run through sand which would significantly slow down the animal. The sand would also prevent the growth of vegetation that could support tall trees, which could be used to disrupt the fence. The sand clearing would also provide the ability to electrify the fences with solar power, utilising the clearing from foliage presented.
Massive conservation projects have relied around single flagship species and the surrounding ecol... more Massive conservation projects have relied around single flagship species and the surrounding ecological niche that supports it. Conservation of giant panda, tiger, and bald eagle are examples of such a species-centric or flagship-species strategy for conservation. While such flagship-species approaches have helped conserve other species that are part of the ecological niche, this strategy fails to address holistic problems of habitat conservation across the globe. In habitats with discontinuity of conserved areas or patchiness of species distribution in a contiguous habitat, focus on a single flagship species would end up being detrimental for the conservation of biodiversity. Flagship-species approach can be a sink for expenditure, where more land could be kept aside for conservation, if we were not focussed on a flagship-species. We are proposing a new approach for conservation based on preservation of large contiguous habitats. Our proposal does not preclude monitoring endangered species but we expect the list to be dynamically updated and not focussed on few relatable species that are “cute” by human standards. This would allow conservation efforts to bear fruits for unnoticed but ecologically more significant microorganisms, flora and non-vertebrate animals, along with vertebrates that are usually the focus of current approaches.
The RNA world concept that self-replicating ribonucleic acid (RNA) molecules are keys to all curr... more The RNA world concept that self-replicating ribonucleic acid (RNA) molecules are keys to all current forms of life on Earth and geneticists could not go further down might have missed out on how evolution has actually happened in real genetic terms.
Out of all hypothesis and proposals, one that stands strong in the debate of “RNA before DNA” is “protein synthesis can occur in the absence of DNA but not in the absence of RNA” . To contest this hypothesis, one should take a close look on life of an RNA molecule and their early degeneration process.
Earlier RNA-protein interaction systems are highly doubtful because RNA is never a long-time informational molecule and even if they are or they used to be, many such information might got lost. Assuming this kind of unstable molecule being the early days primary replication machinery, information contents might have significantly lost and this will again raise a question on how similar or same species maintains identity?
Transferring information outside of the nucleus is only required when there is a nucleus.
Taken together these concepts, we need to revisit the origin of life in newer genetic terms.
JBI is quite an exciting platform to write and I intuitively relate it to my Twitter handle. But ... more JBI is quite an exciting platform to write and I intuitively relate it to my Twitter handle. But this article is much beyond how JBI or any other typical journal works. The idea that a country is making any headway in research and development (R&D) or not is measured by the number of journal articles published from the region, their cumulative impact factors and h-index needs to be shown "Red-flag".
The original measure of the country's progress in R&D could be estimated with the inception of countrywide research publication platforms which will publish articles after rigorous peer-review on various subject lines submitted from that country only. This way, every country gets one.
So what happens to the research coming out of multi-country collaboration?
All participating countries will share the due credit after it is published in the database/platform of lead corresponding author's country. Alternatively, it can get published in the database of the country which funded the research.
What about ISSN numbers, Impact factors and Citations?
Each platform will have an unique identifier number, receive world ranking (no more impact points, 1 is better than 2 here) and the top papers will be judged by the number of times they were cited.
Who will run this?
Preferably government through crowdsourcing.
Gelling agents are required for formulating both solid and semisolid media, vital for the isolati... more Gelling agents are required for formulating both solid and semisolid media, vital for the isolation of microorganisms. Gelatin was the first gelling agent to be discovered but it soon paved the way for agar, which has far superior material qualities. Source depletion, issues with polymerase-chain-reaction and inability to sustain extermophiles etc., necessitate the need of other gelling agents. Many new gelling agents, such as xantham gum, gellan gum, carrageenan, isubgol, and guar gum have been formulated, raising the hopes for the growth of previously unculturable microorganisms. We evaluate the progress in the development of gelling agents, with the hope that our synthesis would help accelerate research in the field.
Many insects, including Drosophila melanogaster, have a rich repertoire of olfactory behavior. Co... more Many insects, including Drosophila melanogaster, have a rich repertoire of olfactory behavior. Combination of robust behavioral
assays, physiological and molecular tools render D. melanogaster as highly suitable system for olfactory studies. The small number
of neurons in the olfactory system of fruit flies, especially the number of sensory neurons in the larval stage, makes the exploration of sensory coding at all stages of its nervous system a potentially tractable goal, which is not possible in the foreseeable future in any mammalian preparation. Advances in physiological recordings, olfactory signaling and detailed analysis of behavior, can place larvae in a position to ask previously unanswerable questions.
Microbial media has undergone several changes since its inception but some key challenges remain.... more Microbial media has undergone several changes since its inception but some key challenges remain. In recent years, there has been exploration of several alternative nutrient sources, both to cater to the specificity in requirement of growth of “fussy microorganisms” and also to reduce costs for large-scale fermentation that is required for biotechnology. Our mini-review explores these developments and also points at lacunas in the present areas of exploration, such as a lack of concerted effort in pH and osmolarity regulation. We hope that our commentary provides direction for future research in microbial media.
Calcium oxalate in plant bodies lead to stones in kidney, upon consumption. Calcium oxalate is fr... more Calcium oxalate in plant bodies lead to stones in kidney, upon consumption. Calcium oxalate is frequently found in plants in the form of tiny needle like raphides. Out of the 5 types of calcium oxalate crystals, raphides are the predominant ones. Calcium oxalate gets incorporated in our body through plant derived food that contains them; a little amount of them is also synthesized in humans endogenously. Both the sources contribute to kidney problems. Occurrence of calcium oxalate is not limited to higher plants only but also extends to algae, fungi and lichens. Out of all the 3 forms of calcium oxalate, monohydrate form is the one widely reported to cause kidney problems. In this study, we review raphides and explore their possible remediation in order to utilize plants of food and medicinal importance the better way. We also review traditional knowledge of raphide neutralization and point to the methods of removal of calcium oxalate and raphides.
A number of web tools are available for the prediction and identification of target microRNAs (mi... more A number of web tools are available for the prediction and identification of target microRNAs (miRNAs). The choice, availability, validity and selection of an optimal yet appropriate tool are a challenge for the design of high throughput assays with promising miRNA targets. The current trends and challenges for target microRNAs (miRNAs) prediction, identification and selection is described in this review.
The oil-rich and weedy plant Jatropha has been hailed as the most promising source of biofuel on ... more The oil-rich and weedy plant Jatropha has been hailed as the most promising source of biofuel on the planet, as a non-food, drought-resistant and oil-rich crop, Jatropha curcas fulfils many of the requirements for biofuel industries.
A better understanding of the biochemical pathway leading to the synthesis of Jatropha oil and its regulation both by exogenous and endogenous factors is essential for facilitating increased yield. Increasing evidence has shown that miRNAs play multiple roles in various biological processes. The research finds previously known miRNAs from various plant species expressed sequence tags (EST) database to search for potential miRNAs and their targets in Jatropha curcus.
Here we present an EST (Expressed Sequence Tags) based homology search approach for the detection of miRNAs and their targets in Jatropha curcas using previously known miRNA sequences from Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Ricinus communis, Citrus sinensis, Vitis vinifera. We find presence of no miRNAs. What can be the cause?
Gene regulation is vital for life and it involves plethora of mechanisms, including microRNA (miR... more Gene regulation is vital for life and it involves plethora of mechanisms, including microRNA (miRNA) based RNA inhibition. Messenger RNA (mRNA) inhibition by miRNA requires less sequence specificity than inhibition by small inhibitory RNA (siRNA) and has different set of enzymes required for processing. The regulation and richness of RNA inhibition and specifically miRNA action is just beginning to be studied, while much work has undergone in the study of synthesis and processing of miRNA. More than 1800 unique human miRNAs have been computationally predicted and several have been experimentally validated. Given their ability to act as sequence specific regulators of the transcriptome, miRNAs have potential in therapeutics and diagnostics. We specifically focus on synthesis of current therapeutic applications of miRNA. We discuss the two different strategies in miRNA treatment: mimics and antagonists, and bring forward the promises and perils of miRNA therapy in its journey from lab to medicine.
Electric fences have been used more successfully than non-electric fences in comparable settings ... more Electric fences have been used more successfully than non-electric fences in comparable settings for a variety of animals. The frequent breaking of electric fences by large mammals such as elephants that can pull a tree down on the fence, or rhinos that can run through fences with impunity, decrease the effectiveness of electric fences. Laying out a depressed region near the fence with the width more than the tallest tree, and filling it with sand would increase the effectiveness of electric fences. This would force the animal to run through sand which would significantly slow down the animal. The sand would also prevent the growth of vegetation that could support tall trees, which could be used to disrupt the fence. The sand clearing would also provide the ability to electrify the fences with solar power, utilising the clearing from foliage presented.
Massive conservation projects have relied around single flagship species and the surrounding ecol... more Massive conservation projects have relied around single flagship species and the surrounding ecological niche that supports it. Conservation of giant panda, tiger, and bald eagle are examples of such a species-centric or flagship-species strategy for conservation. While such flagship-species approaches have helped conserve other species that are part of the ecological niche, this strategy fails to address holistic problems of habitat conservation across the globe. In habitats with discontinuity of conserved areas or patchiness of species distribution in a contiguous habitat, focus on a single flagship species would end up being detrimental for the conservation of biodiversity. Flagship-species approach can be a sink for expenditure, where more land could be kept aside for conservation, if we were not focussed on a flagship-species. We are proposing a new approach for conservation based on preservation of large contiguous habitats. Our proposal does not preclude monitoring endangered species but we expect the list to be dynamically updated and not focussed on few relatable species that are “cute” by human standards. This would allow conservation efforts to bear fruits for unnoticed but ecologically more significant microorganisms, flora and non-vertebrate animals, along with vertebrates that are usually the focus of current approaches.
The RNA world concept that self-replicating ribonucleic acid (RNA) molecules are keys to all curr... more The RNA world concept that self-replicating ribonucleic acid (RNA) molecules are keys to all current forms of life on Earth and geneticists could not go further down might have missed out on how evolution has actually happened in real genetic terms.
Out of all hypothesis and proposals, one that stands strong in the debate of “RNA before DNA” is “protein synthesis can occur in the absence of DNA but not in the absence of RNA” . To contest this hypothesis, one should take a close look on life of an RNA molecule and their early degeneration process.
Earlier RNA-protein interaction systems are highly doubtful because RNA is never a long-time informational molecule and even if they are or they used to be, many such information might got lost. Assuming this kind of unstable molecule being the early days primary replication machinery, information contents might have significantly lost and this will again raise a question on how similar or same species maintains identity?
Transferring information outside of the nucleus is only required when there is a nucleus.
Taken together these concepts, we need to revisit the origin of life in newer genetic terms.
JBI is quite an exciting platform to write and I intuitively relate it to my Twitter handle. But ... more JBI is quite an exciting platform to write and I intuitively relate it to my Twitter handle. But this article is much beyond how JBI or any other typical journal works. The idea that a country is making any headway in research and development (R&D) or not is measured by the number of journal articles published from the region, their cumulative impact factors and h-index needs to be shown "Red-flag".
The original measure of the country's progress in R&D could be estimated with the inception of countrywide research publication platforms which will publish articles after rigorous peer-review on various subject lines submitted from that country only. This way, every country gets one.
So what happens to the research coming out of multi-country collaboration?
All participating countries will share the due credit after it is published in the database/platform of lead corresponding author's country. Alternatively, it can get published in the database of the country which funded the research.
What about ISSN numbers, Impact factors and Citations?
Each platform will have an unique identifier number, receive world ranking (no more impact points, 1 is better than 2 here) and the top papers will be judged by the number of times they were cited.
Who will run this?
Preferably government through crowdsourcing.
Gelling agents are required for formulating both solid and semisolid media, vital for the isolati... more Gelling agents are required for formulating both solid and semisolid media, vital for the isolation of microorganisms. Gelatin was the first gelling agent to be discovered but it soon paved the way for agar, which has far superior material qualities. Source depletion, issues with polymerase-chain-reaction and inability to sustain extermophiles etc., necessitate the need of other gelling agents. Many new gelling agents, such as xantham gum, gellan gum, carrageenan, isubgol, and guar gum have been formulated, raising the hopes for the growth of previously unculturable microorganisms. We evaluate the progress in the development of gelling agents, with the hope that our synthesis would help accelerate research in the field.
Many insects, including Drosophila melanogaster, have a rich repertoire of olfactory behavior. Co... more Many insects, including Drosophila melanogaster, have a rich repertoire of olfactory behavior. Combination of robust behavioral
assays, physiological and molecular tools render D. melanogaster as highly suitable system for olfactory studies. The small number
of neurons in the olfactory system of fruit flies, especially the number of sensory neurons in the larval stage, makes the exploration of sensory coding at all stages of its nervous system a potentially tractable goal, which is not possible in the foreseeable future in any mammalian preparation. Advances in physiological recordings, olfactory signaling and detailed analysis of behavior, can place larvae in a position to ask previously unanswerable questions.
Microbial media has undergone several changes since its inception but some key challenges remain.... more Microbial media has undergone several changes since its inception but some key challenges remain. In recent years, there has been exploration of several alternative nutrient sources, both to cater to the specificity in requirement of growth of “fussy microorganisms” and also to reduce costs for large-scale fermentation that is required for biotechnology. Our mini-review explores these developments and also points at lacunas in the present areas of exploration, such as a lack of concerted effort in pH and osmolarity regulation. We hope that our commentary provides direction for future research in microbial media.
Calcium oxalate in plant bodies lead to stones in kidney, upon consumption. Calcium oxalate is fr... more Calcium oxalate in plant bodies lead to stones in kidney, upon consumption. Calcium oxalate is frequently found in plants in the form of tiny needle like raphides. Out of the 5 types of calcium oxalate crystals, raphides are the predominant ones. Calcium oxalate gets incorporated in our body through plant derived food that contains them; a little amount of them is also synthesized in humans endogenously. Both the sources contribute to kidney problems. Occurrence of calcium oxalate is not limited to higher plants only but also extends to algae, fungi and lichens. Out of all the 3 forms of calcium oxalate, monohydrate form is the one widely reported to cause kidney problems. In this study, we review raphides and explore their possible remediation in order to utilize plants of food and medicinal importance the better way. We also review traditional knowledge of raphide neutralization and point to the methods of removal of calcium oxalate and raphides.
A number of web tools are available for the prediction and identification of target microRNAs (mi... more A number of web tools are available for the prediction and identification of target microRNAs (miRNAs). The choice, availability, validity and selection of an optimal yet appropriate tool are a challenge for the design of high throughput assays with promising miRNA targets. The current trends and challenges for target microRNAs (miRNAs) prediction, identification and selection is described in this review.
The oil-rich and weedy plant Jatropha has been hailed as the most promising source of biofuel on ... more The oil-rich and weedy plant Jatropha has been hailed as the most promising source of biofuel on the planet, as a non-food, drought-resistant and oil-rich crop, Jatropha curcas fulfils many of the requirements for biofuel industries.
A better understanding of the biochemical pathway leading to the synthesis of Jatropha oil and its regulation both by exogenous and endogenous factors is essential for facilitating increased yield. Increasing evidence has shown that miRNAs play multiple roles in various biological processes. The research finds previously known miRNAs from various plant species expressed sequence tags (EST) database to search for potential miRNAs and their targets in Jatropha curcus.
Here we present an EST (Expressed Sequence Tags) based homology search approach for the detection of miRNAs and their targets in Jatropha curcas using previously known miRNA sequences from Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Ricinus communis, Citrus sinensis, Vitis vinifera. We find presence of no miRNAs. What can be the cause?
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Papers by Nabajit Das
Out of all hypothesis and proposals, one that stands strong in the debate of “RNA before DNA” is “protein synthesis can occur in the absence of DNA but not in the absence of RNA” . To contest this hypothesis, one should take a close look on life of an RNA molecule and their early degeneration process.
Earlier RNA-protein interaction systems are highly doubtful because RNA is never a long-time informational molecule and even if they are or they used to be, many such information might got lost. Assuming this kind of unstable molecule being the early days primary replication machinery, information contents might have significantly lost and this will again raise a question on how similar or same species maintains identity?
Transferring information outside of the nucleus is only required when there is a nucleus.
Taken together these concepts, we need to revisit the origin of life in newer genetic terms.
The original measure of the country's progress in R&D could be estimated with the inception of countrywide research publication platforms which will publish articles after rigorous peer-review on various subject lines submitted from that country only. This way, every country gets one.
So what happens to the research coming out of multi-country collaboration?
All participating countries will share the due credit after it is published in the database/platform of lead corresponding author's country. Alternatively, it can get published in the database of the country which funded the research.
What about ISSN numbers, Impact factors and Citations?
Each platform will have an unique identifier number, receive world ranking (no more impact points, 1 is better than 2 here) and the top papers will be judged by the number of times they were cited.
Who will run this?
Preferably government through crowdsourcing.
assays, physiological and molecular tools render D. melanogaster as highly suitable system for olfactory studies. The small number
of neurons in the olfactory system of fruit flies, especially the number of sensory neurons in the larval stage, makes the exploration of sensory coding at all stages of its nervous system a potentially tractable goal, which is not possible in the foreseeable future in any mammalian preparation. Advances in physiological recordings, olfactory signaling and detailed analysis of behavior, can place larvae in a position to ask previously unanswerable questions.
A better understanding of the biochemical pathway leading to the synthesis of Jatropha oil and its regulation both by exogenous and endogenous factors is essential for facilitating increased yield. Increasing evidence has shown that miRNAs play multiple roles in various biological processes. The research finds previously known miRNAs from various plant species expressed sequence tags (EST) database to search for potential miRNAs and their targets in Jatropha curcus.
Here we present an EST (Expressed Sequence Tags) based homology search approach for the detection of miRNAs and their targets in Jatropha curcas using previously known miRNA sequences from Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Ricinus communis, Citrus sinensis, Vitis vinifera. We find presence of no miRNAs. What can be the cause?
Out of all hypothesis and proposals, one that stands strong in the debate of “RNA before DNA” is “protein synthesis can occur in the absence of DNA but not in the absence of RNA” . To contest this hypothesis, one should take a close look on life of an RNA molecule and their early degeneration process.
Earlier RNA-protein interaction systems are highly doubtful because RNA is never a long-time informational molecule and even if they are or they used to be, many such information might got lost. Assuming this kind of unstable molecule being the early days primary replication machinery, information contents might have significantly lost and this will again raise a question on how similar or same species maintains identity?
Transferring information outside of the nucleus is only required when there is a nucleus.
Taken together these concepts, we need to revisit the origin of life in newer genetic terms.
The original measure of the country's progress in R&D could be estimated with the inception of countrywide research publication platforms which will publish articles after rigorous peer-review on various subject lines submitted from that country only. This way, every country gets one.
So what happens to the research coming out of multi-country collaboration?
All participating countries will share the due credit after it is published in the database/platform of lead corresponding author's country. Alternatively, it can get published in the database of the country which funded the research.
What about ISSN numbers, Impact factors and Citations?
Each platform will have an unique identifier number, receive world ranking (no more impact points, 1 is better than 2 here) and the top papers will be judged by the number of times they were cited.
Who will run this?
Preferably government through crowdsourcing.
assays, physiological and molecular tools render D. melanogaster as highly suitable system for olfactory studies. The small number
of neurons in the olfactory system of fruit flies, especially the number of sensory neurons in the larval stage, makes the exploration of sensory coding at all stages of its nervous system a potentially tractable goal, which is not possible in the foreseeable future in any mammalian preparation. Advances in physiological recordings, olfactory signaling and detailed analysis of behavior, can place larvae in a position to ask previously unanswerable questions.
A better understanding of the biochemical pathway leading to the synthesis of Jatropha oil and its regulation both by exogenous and endogenous factors is essential for facilitating increased yield. Increasing evidence has shown that miRNAs play multiple roles in various biological processes. The research finds previously known miRNAs from various plant species expressed sequence tags (EST) database to search for potential miRNAs and their targets in Jatropha curcus.
Here we present an EST (Expressed Sequence Tags) based homology search approach for the detection of miRNAs and their targets in Jatropha curcas using previously known miRNA sequences from Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Ricinus communis, Citrus sinensis, Vitis vinifera. We find presence of no miRNAs. What can be the cause?