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Current Topics in Synthetic Biology Theory and Practice:
(see: MEDBIOS) continues the scientific documentation from investigating metabolises and cell modelling and its various players in various areas of neurological brain function, cancers, nutrient-disease interactions and the aging process, amongst others.
- Section I Neuropharma and Cognitive Enhancement Therapeutics in Psychosocial & Kinesiological Rehabilitation
- Section II Neurhormonal Immunomodulation
- Section III Molecular Medicine and Nutrigenomics
Section I. We are currently investigating a recent report that has surfaced, but nevertheless rare medical condition or phenomenon where brain concussion or 'knock-out' (unconsciousness) can lead to over-compensation upon apparent recovery and overactivation of brain centre(s) and function(s). One e. g. is perceiving fractal geometries in everyday objects, not perceived before. The second e. g. we have evidence for are under two 'equilibrated' drug regimens using two relatively new anti-psychotics, like Invega (generic drug name), and that mental function such as information processing so as to perform everyday tasks or activities, is activatable (see: MEDBIOSE) and/or maintainable. These reports corroborate new ones with use of these drugs in practice amongst other mental health consumers in the community. It would be of further interest to probe what if any neuropeptides, neurhormones and balance of neurotransmitters and if in the long term developmental changes occur in the brain's neuro-circuitry subject to severity. Note, the LMW-proteome in circulating in the bloodstream is just beginning to be investigated from the brain, an e. g. of which are the stress hormones.
Cognitive enhancers are coming now into the fore and are also within theories of 'plasticity' of brain structure and function. We have always speculated as to whether cognitive enhancers (e. g. processing, problem solving, storage, and retrieval functions) earlier on have further down the line could have a neuroprotective effect, a new frontier of research in neuroscience, against Alzheimers or other dementias. We speculate that dementias are a type of developmental disorder of the brain to be protected against onset or progression. The brain progresses in stages as it is hypothesized we have put forward new concepts of: cognitive enhancement, neuroplasticity, neurodevelopmental disorders and neuroprotective interventions.
The recent studies of Reelin proteins in the brain that can reverse the overt signs of abberant cellular anatomical plaque and amyloid-beta fibril entanglements can 'reverse' this clinical phenotype of Alzheimers via the Reelin cell signaling pathways and recovery of cognate cognitive deficits. (See also the story by pasting this link on you browser: http://www.ub.edu/web/ub/en/menu_ eines/noticies/2014/03/010.html.
Section II. Biopharmacogeneic Therapeutic Activation of the Cellular Immune System. The humeral immune response system model rudiments: --Cytotoxic T cells recruited by helper T cells (initiates T and B cells) kills infected body cells by pathogens or invaders (parasitic, bacterial and viral) --Natural killer (NK) cells recognizes and kills cells infected by a broad range of invaders --Killer (K) cells also kills infected cells coated with antibodies X-reacted with their antigenic determinants --Biopharmacogeneic drugs that effect cell signalling activating cellular immunity --Cytotoxic complement-like cell destruction by humeral cellular factors --Cancer (melanoma) is acted on by circulatory leukocyte and endothelial cells (as a model) --At this time there are regulatory homeostatic factors that affect phagocytosis such as calreticulin; what factors for enhancement and/or optimization are possible together with bio-pharma in biotech is a question. T, B, NK, and K cells, complement, and phagocytosis all are involved in the total immunogeneic response. The most recent news to come out of Skye Blue in regards to our hypothetical modeling of sheep immunogeneic cell lines is as follows: 1) a humeral haemocytotic germinal cell line primed with hormonal cell blockers to growing cancer cells; could an e. g. be anti-CD47 signaling agent or hormone encouraging an effective macrophagic phagocytotic outcome, 2) a systemic CNS –sourced neurhormonal activation of complement cytotoxicity and phagocytosis of cancer cells (an e. g. in the literature is with acetylcholine and other anti-tumour cytotoxic T-cell immune response mechanisms).
SKYENEWS: It has come to our attention at Skye Blue in the recent year that new evidence using epidural delivery via lumbar (as in lower back section of the spine) puncture into cerebrospinal fluid (CSF) space of an engraft from mononucleocytes from umbilical (as in fetus) cord blood cells results in successful engraftment and restoration of partial function (albeit, not as a cure per se- as of yet, anyways) of bodily motor functions and with injection of lithium and further training or exercise. The cells, once taken to the surrounding tissue, stimulates formation of 'long tracts' along the spinal cord either directly stimulating regeneration of spinal cord cells or indirectly via perhaps other spinal cord cells via certain yet to be defined growth factors. Lithium has the added effect of causing the engrafted cells to stimulate the spinal cord cells to regenerate through such growth factors. Methylprednisolone administered allows prolonged half-life of cord blood cells as engrafted to take effect. This study and others like it would demonstrate extremely thought-provoking speculation as to what growth factors in the CNS and peripheral nervous system could be and including established and yet to be discovered neurhormones in circulation and what their nature or functions are, with the depleted circulating [LMW]-proteome in the blood supply across the blood-brain barrier, in the general circulation and in the CSF spaces. And now for the 'piece de resistance' of the story: the momentous question at Skye Blue is that of the nature of the so-called 'mind-body' axis and, in particular, does the brain communicate directly to the 'lower body functions' via direct innervation and/or via the circulation through a related group of released growth factors and/or neurhormones postulated earlier in the phenomenon called immunomodulation towards, for e. g., the development of the immune system to maturity (viz. adapted, innate, humeral and cellular immunity) and further our suggestion that this offers perspectives towards a framework for manipulation towards boosting (or optimizing) in future anti-viral therapies and cancer treatments, which may arrive sooner than we might expect.
Section III. "Chronic Inflammation, Immunogeneicity and Disease: the promise of new drug discovery." We are publishing this new paper on the links between chronic inflammation, immunogeneic response and disease states, such as diabetes, atherosclerosis and cancer, and their links to both nutritionals, Vit D and fructans, in the lower gut, a clue to the linkage between the two factors and other diseases also linked to the prolonged chronic elicitation or aggravation of the inflammation response. We invite editorial oversight on the investigation of the inflammation process including published/unpublished research findings on this exciting and growing field in health research. There are new monoclonal antibodies administered by subcutaneous injection that can be used against products of genes that help activate inflammation or possibly act to enhance the production of gene products that help modulate the inflammation cascade, with nutritionals. Vaccines would of course not be a functional route, unlike the in vitro, ex vivo therapeutic modality of producing monoclonal antibodies. The immune response as outlined and small molecules in the inflammatory response could interact in future drug trials and thus affect immunogeneicity in a negative way in fighting disease. Systemic inflammatory response syndrome (SIRS) could be used as a model for the study of whether drug trials will have this issue of interactions with the immune system and affect disease fighting ability of the body. The cytokine storm as described elsewhere is an uncontrolled feedback cascade eliciting T cell response and macrophages to the site of infection; however, over response can lead to complications and even death. (Thank you to our respondent who mentioned with the Wordpress.com blog feedback on the 'cytokine storm'.)
In our continued search and development with the use of synthetic biology for the advancement of Vit D activated-forms of the drugs and their pharmacogenic effects to T2Diabetes, atherosclerosis and heart disease or health (in general) and cancers, including lower bowel cancer, we propose a precursor derivative (a steroidal 'lipoic' aldehyde) synthesized (see: Flores, 1980, Kalamazoo College MI U.S.A.) through the body's natural metabolic synthetic pathways to Vit D's activated forms to act as 'agonistes' against the feedback inhibition (FBI) to the drug with <increases in effectivity in therapeutic indices>. There are, as we speak, alternative approaches which may be less effective using Vit D at its receptors for various tissues types and/or gene-selectivity with Vit D receptor modulators (VDRMs) that act with ligands (it is interesting to note here that recent use of non-seco-steroidal VDR ligands, unlike activated forms of steroid-like Vit D, have been developed for this) resulting in their increased effect. Synthetic biology uses chemical protocols and inferences to solve mechanistic problems useful for medicinal chemistry. There are two sides to this problem on the sterol lanosterol. Problem A will involve lanosterol and its synthesis with reduction of C-25 on the side-chain. If resynthesized and a 13C label placed on the side-chain on C26 the reduction of the alpha-beta unsaturation on its plane would result in a chiral centre determining if the H is introduced above as opposed to below the plane of symmetry. A 13C NMR scan would show the position of the lone peak upstream or downstream depending on nuclear shielding. The last step is in question as to whether a Wolff-Kishner Reduction is an effective route or whether the one-pot reduction with solvent n-butyl silane or diethyl silane (Si-H) that reacts 1H per -OH group and sequentially 2H per carbonyl group using the catalyst tri(pentafluorophenyl)-borane. The phenols are converted to silyloxybenzenes. Problem B with synthetic biology in this work is to synthesize a derivative of a precursor to Vit D's active compounds through the liver/kidneys that back inhibits (feedback inhibition, FBI) as an 'agonist' and could be a candidate as a pro-Vit D therapeutic drug. We are "christening" these class of drugs at this juncture by commercial name: Retonibionols (R). A major hurdle of this type of research is with animals that starts with lanosterol (animals and fungi) which convert this to cholesterol via the cytochrome P-450 superfamily of enzymes in 19 steps (drugs in pharma can take typically up to 21 steps) and to 7-dehydrocholesterol and upon irradiation to cholecalciferol or Vit D3 and to related hormones like calcidiol in the liver and kidney. Enzyme affinity and avidity to drug analogues is a question open to experimentation with structure-mechanisms to be studied with the enzymes involved in proteomics, structural folding studies, x-ray crystallography and structure-proofing to make the lanosterol side-chain derivatives bind constructively by residue replacement. Orientation and proximity (e. g. hydrogen-bonding between the aldehyde group of the prosthetic side-chain and amino acid residues of the enzymes) of atomic residues is apropos here. Steroidals such as those derived and proposed from Vit D activated forms can open up further speculation as to their appropriateness for heart health or cardiac performance, muscular performance and inflammation and cancer. All these new avenues of research will have to be further studied.
We are also attempting breaking new ground in the bioengineering of metabolism in animal livestock, as well, including the area of energy metabolosomics and engineering energy use with better productivity in terms of inputs including uptake, utilization and regulatory factors. Thermogenic homeostasis is a factor and so with its evolution in excess. There is prebiotic rumen microbial data with water-soluble carbohydrates (WSC) and pre-formed amino acids (PFAAs) increasing metabolic efficiency and growth. One wonders what lies ahead in its molecular biology. In reference to the portfolio of projects (See: Projek Konsep) on probiotics and the new emerging field of nutrigenomics and meat science that it plays in nutritional supplementation there is an important breakthrough in the possible use of VitD, fructan and folate, as examples, of recent studies with their role with the VDR receptor for VitD between it and fructan and cell signaling pathways and a possible use for energy conservation and greater microbial cell protein (MCP) synthesis in digestion of ruminant livestock and in meat production using recombinant gene manipulations to code for production of these co-factors. There has been evidence to show in microbial culture that, for example, rumen microbes that function to breakdown fibre and contribute substantially to MCP synthesis via use of pre-formed amino acid [peptides + free amino acids] can be used as cellular models and so with evidence involved with fructan and related WSC. The role of cofactor-enzyme interactions has to be biochemically explored and documented involved specifically in energy cell metabolism. Which is (part of) the proposed hypothesis on this matter. And further studies from McGill U. (1980) in their biomedical areas at the Dept. of Biochemistry: folate and energy metabolism have also been linked. Are there networks in folate-related metabolism that link together in regards to use of ATP in terms of: cell membrane (CM) transport processes, cellular catabolism and/or anabolism and cell mitogenesis or reproduction. We hope that this will contribute revolutionary finds towards more sustainable practices in animal protein production in solving economic demands and world hunger, in general. Both the use of biocropping, which has begun, microbial GMO biotechnology in animal feeding, still in its nascency, and newer approaches to making an GMO animal livestock spp. nutritionally enriched with protein, vitamins and minerals may be new breath to an old convention based on true and very specific metabolic engineering of both components and its systems approach.
SKYENEWS: In a recent review (2012) it has been suggested that functional foods such as VitD and fructan (FOS) be now measured as to their effects via "gold standard" measurements as with chemokines and cytokines (e.g. ILs), are define inflammatory or anti-inflammatory (e. g. fish sauce proteins lead to increase in the type of characteristic markers that are described as anti-inflammatory). In a very recent review from Quebec, Canada researchers in 2014 studied dairy and its products have been more closely correlated between those natural ingredients and inflammatory markers (above) which are: TNF-alpha, IL1-beta, Il-6, Il-8, MCP-1, and as opposed to IL-10, which is considered anti-inflammatory. The overall picture of VitD/fructan and their effect on chronic inflammation and disease aetiology (see: here, elsewhere) leads one to think about the very possibilities of such schema for such "gold standards" in blood measurements upon ingestion of functional foods. The inflammatory profile from the blood biochemical profiles of how high/low these inflammatory markers are vs. anti-inflammatory markers could served as a starting schema. It should be added that the organ that comes to mind here first of all amongst others would be the lower G.I. tract which have measurable glycan-type receptors for FOS and nuclear steroid or VitD receptors (VDRs) in the gut lining to bring about cell signaling. Which brings us further to the point of which operative drug agents (small organic molecules) that could be designed to bring about functional food-type, anti-inflammatory action over the long term to prevent, alleviate or help bring about a cure to chronic inflammatory-type diseases in various organ tissues such as atherosclerosis, diabetes type-II and colonic cancers. There is also question further to this here as to how to fortify plant products with the family of phytosterols, including VitD, and for that matter fructan and other fat-soluble vitamins and minerals (note:beta-carotene from daffodil has already been considered a success to be tested in India in future and further what with the new developments oto use genome engineering) that have similar effects like VitE to be anti-cancer and have wildly great potential in huge middle class markets in the developing world for multi-nationals wishing an ROI on earlier crop R&D development. Cows milk could also be enriched in our view not by what could be more slow, less effective breeding programmes for anti-inflammatory milk-type protein-enriched milk products using the more publicly acceptable genome engineering techniques which are likely to be reconsidered seriously commercially by the USDA in the coming years as just one of the agenda items with SkyeBlue in genome engineering and using amongst other strategies like disease resistance and increased hardiness and greater productivity in plant or crop and animal biotechnology.
OUR NEW PLANNED PUBLICATION ON ENSILAGE (2019), Springer-Verlag (FRG), Applied Microbiology and Biotechnology: "dsRNA Technology for Silage (temperate and tropical) and their Processing and Rumen Digestion: a minireview," by D. A. Flores.
We are sending this communication to update you on our progress here at Skye Blue on the area covering a mini-review on 'open' invitation from Springer-Verlag (FRG) with our title: "dsRNA Technology for and Silage (temperate and tropical) and their Processing and Rumen Digestion: a minireview," by D. A. Flores.
We will discuss biotechnology, excluding prebiotic dsRNA approaches to improve silages in tropical and temperate countries and the use of dsRNA with probiotic microbial agents to aid in their rumen digestion. In the tropics haymaking with the availability of sun would be the method of choice in processing/storage of the crop but in areas where there is a wet season such as in South Africa, Western Australia and southern China ensilage with the wet crop would be another option. Where feeding is throughout the year, and mechanization is available, there is the alternative of ensilage by harvesting, then storage via ensiling, and then twice feeding in the previous wet season and then the dry season following. Different whole plant silages will be discussed, or in part, composed of leaves, sheath, grain, cob. The various silages are usually, as classified in this paper, green and/or leafy silages and FCR or fibrous byproduct tropical silages, pre-treated and supplemented with ammonia-N, such as ammoniation. I. Rice Straw: The demographics in terms of world-wide production and potential as a feed resource in developing countries where low-quality feeds are the norm is great. II. Grasses & Legumes: the yield of C4 and C3 grasses and nutritive value and ensiling practices including their improvement where non-GMO technologies are issues with ensilage where boosting feed supply is of the essence (e. g. approaches to boosting C-sinking). III. Whole Plant Maize. High moisture ear corn (HMEC) and low-lignin cob that is non-GMO manipulated and bred are new applications for high energy feeding for growing calves. Grain silos could be a practical means of storing/handling this crop in developing countries used for concentrate feeding. Sale of this commodity makes farming maize an attractive commercial proposition for small farmers in the tropics. IV. Wheat. FCR straw ensilage in the tropics would follow along the same practices as rice straw if developed countries find a need for use of more sustainable feeding practices given demographic and environmental factors on land-food systems, the relative commodity prices of grains and forages (grazed, haylage, silage) and perhaps effects of global warming may have on cropping. V. Sorghum. Excellent wet ensilage can be practised with this crop. Quality and characteristics with ensiling practices will be discussed including use of stalk or stems which are sugar-rich. VI. Whole Plant Plantain. The fruit when green has tannins which can interfere with protein digestibility. The leaves and sheaths with their fibre content if improved with biotechnology during ensilage show great potential. Banana stalk is also an agri-waste feedstock that can be pre-treated with ligninolytic enzyme technology. VII. Applications of Ensilage Treatment with Acidification. Acidification to stabilize the ensiling mass with available sugars which may be lacking (i. e. water-soluble carbohydrates, WSC) and protecting protein from breakdown (pre-formed amino acids, PFAAs) by field-drying green fodders are factors that increase the efficiency of microbial cell protein (MCP) synthesis in the rumen. The use of fibrolytics such as EFE treatment and fungal innoculants to increase the free sugar availability should result in decreased ammonia-nitrogen (N) and increased volatile fatty acids (VFAs) production as this relates to the ruminal efficiency of digestion. Transport processes of amino acids (AAs) may be limiting the efficiency of MCP synthesis. The concentration of PFAAs in rumen fluid has been found to be insignificantly low to measure as a parameter. VIII. The annexation of genetically manipulated lignases with urea-ammoniation of straw, a form of tropical ensilage, where ambient temperature and moisture conditions are conducive, is an application with feeds pre-treatment. IX. Probiotics in Rumen Digestion. Progress is discussed. Yeast and fungal probiotics, as fed, are the only ones that have successfully persisted in the rumen (RJ Wallace et al., 1978) in the field, making them a commercially viable proposition.
New Approaches to dsRNA Regulatory Manipulation of Rumen Microbes.
1) NEW. Yeast, an e. g. of which is Saccharomyces cerevisiae, fed continuously at 5g/d with an Fae enzyme and an E. coli etherase can be cloned by precision editing in this host to improve fibre digestion attacking the carbohydrate-lignin complexes in plant residues.
2) NEW. Yeast, an e. g. of which is Saccharomyces cerevisiae fed continuously at 5g/d with a grass diet that are low in certain essential amino acids (E.A.A.) by boosting total E.A.A. flows to the intestines by adding E.A.A. operon cassettes that are limiting in microbial protein synthesis (see: Flores 1989), fed with ATP energy from the increase in fibre digesters that result from yeast addition, increasing the sugar energy pool that would support amino acid synthesis and microbial growth.
3) NEW. Aspergillus oryzae is known to retain like yeast in the rumen and will be fed at a given rate (g/d). To provide A. oryzae as a 'surrogate' for the well-known protein MB-1 it is unknown at this time if it can retain in the rumen although 'tweaking' the energy supply pool, e. g., adding an additional cellobiase gene which increases energy availability from fibre by deregulation of feed-back inhibition (FBI) might serve this purpose (see: Flores, 1988, MAppSc thesis).
These are all here-to-fore untested options. We believe there is a moratorium on any further genetic engineering in the rumen (consulting ILRI, Addis Ababa, Ethiopia for any further advise and opinions on this matter is suggested).
Oligosaccharides & Peptides/Amino Acids and Possible Effects on Cell Proliferation.
Genomic sequencing with analyses of specific genes using a microarray approach with rumen microbial cell modeling, similar to mammalian cells, for putative products archaetypical in procaryotic rumen microbial cells, that will require significant investigation as was discovered for mammalian p38, MK2 and alpha-TNFproducts and a 3'-UTR sequence, with an ARE sequence, that is untranslated coding for a transcript that normally suppresses alpha-TNF products implicated in mitogenesis, with the correlation of treatment effects in in vitro culture with inulin (e. g. +fructan in complete media) and pre-formed amino acids (peptides or +peptones in basal media). There are several reviews (see: G. Pang et al., 2012) one that implicated the role of receptors or proteins in the gut (G.I. tract) serving to translocate intracellularly to the nucleus as transcription factors (TFs) that may suggest further details as to how this proposed mechanism might work. p38 as a member of the major MAPK family of proteins would be involved with fructan and pre-formed amino acids targeting receptor proteins that act in cell signaling with p38 metabolically through known modifications of enzymes and other binding proteins and/or their subunits, for e. g., via phosphorylation with kinases and/or acetylation of sugars, which is possible.
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Last update of this entry: September 03, 2018