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registry of biomedical companies

  September 17, 2019
promoting the transfer of scientific know-how between industry and academia
Registry of biomedical companies:

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SKYEVIEW: Comparative approaches to feeding and feed improvement are beneficial in the following order: 1) pre-treatments (viz. biological, chemical, physical and thermal, of which chemical is the most cost-effective), 2) genetically modified (GM) pre-biotic approaches to feeds which benefit digestive fermentation (e. g. water-soluble carbohydrates (WSC) and non-structural carbohydrates (NSC), surrogate proteins, ionophores and low-lignin), 3) protein, energy concentrate supplementation (e. g. by-product feeds such as rice pomace, cassava pomace, palm kernel, leucaena leaf meal) and 4) theoretical/practical feeding of GM pro-biotics boosted for digestion of structural carbohydrates and lignin and 'storage' proteins.  This subject matter is still new and requires considerable input which we invite from our viewing audience.

SKYEVIEW: The whole movement in biotech cropping and plant protection with pest management has been as recent with Bt corn, wheat resistant to rust infestation and now just in soybean and nematode infection.  It was noted by one of our researchers that wheat rust resistance is a world stage issue in food security and time is running to find cultivars resistant with the so-called multiple resistance factors both in wild type and inbred strains and defining their mechanisms at the molecular level. Both foundations in the U.K. and the Bill and Melinda Gates Foundation Inc. USA have undertaken grant funding.  Nematode research is beginning at Monsanto with interests in soybean research in places like Brazil and finding ways to assay the egg count in infected planted soils with advanced biotech (there is an invitation from IdeaConnection.com to submit leads for research in this area) and finding mechanisms in natural nematocides in soybeans against the eggs which are the likely target of such agents.

SKYEVIEW: The renewed use of proteomics should be directed to a search for the 'holy grail' of cereal biology regards the grain and its constitutive parts and protein products that can accelerate productive output comparing known 'models' from earlier research on cancer and development applied to plant crops and their growth as well as species in weeds and other plants such as the daffodil, bamboo or the sunflower. Gene-specific promoters and specificity will play a key role in providing means for search of such mechanisms.  It is with great speculation as to the fecundity that can be obtained from results of such research on hyper-accelerated crop yield and production and 'pleiotropy' or its effects on the metabolosome and with its perturbed regulation. The yield increment vs inputs [urea for nitrogen-phosphorous-potassium (N-P-K) and other energy inputs] ratios will measure the sustainabilities obtained with innovation.

SKYEVIEW: The bioengineering of plants for biomass for both food & energy (viz. in marginalized lands) (e. g. root crops, corn, sorghum, sugarcane, miscanthus & switchgrass) is now projected.  Crops in temperate climes where photosynthetic activity is boosted for production and for less H2O loss (transpiration) in the more humid, night hours, allowing for diminished rainfall in America's breadbasket by 2080 will be possible with CAM (Crassulacean acid metabolism) photosynthesis, a type of photosynthesis that evolved in plants that grow in arid conditions where transpiration occurs during the night (rather than day time) and around the Rubisco protein, for greater photosynthesis.

SKYEVIEW: Recent finds studying cellulolytics in the rumen and their interaction with pre-formed amino acid nitrogen (PFAA-N) and attempts to tie in treatments to slow protein degradation and make them more available for rumen microbial uptake during digestion show in certain cases stimulation of PFAA-N uptake by cellulolytics and also for water soluble carbohydrates (WSCs) in perennial rye grass varieties where digestibility and later lactation is significantly improved accompanied by increased dry matter digestibility (%DMD), neutral detergent fibre (%NDF) and acid detergent fibre (%ADF) digestibilities.

SKYEVIEW The current approach to chemically-controlled ensilage in grasses and legume fodders independent of weather conditions at harvest has been via the addition of sugar substrates such as molasses and concentrate (e. g. milled grain) although genetically modified biocrops are a possibility using current tools of maternally segregated chloroplastid DNA 'encapsulated' from genetic drift and safely with biolistic transformative techniques that only act when released at harvest, i. e. those enzymes that degrade buffering capacity from citrate, malate and glycerate.  Malate dehydrogenase is one example of such an enzyme.  Other microbial systems are currently being investigated to find and annotate via bioinformatic genomics the correct genes for the enzyme(s) responsible for buffer degradation.

SKYEVIEW: The search for idiotypic determinants on protozoan cell surfaces to control them immunologically in the rumen will be used first with use of fluorescent-tagged anti-bodies (Abs) in an assay for transport, structural and enzymatic surface proteins.  Those closest to the surface with greatest surface area and affinity will be chosen and possibly porins or ion channel and other transport system proteins.  Monoclonals will be used for this assay.  The question arises what correlates between in vivo and in vitro studies of this reaction, i. e. an assay with fluorescent tagged immunoglobulins (Igs) derived from rumen fluid will be used for this correlation.

SKYEVIEW: A new development at Skye Blue with pre-biosis and biocropping programming for ensilage with subsistence traits that are so-called pro-poor or friendly such as down-regulated protease activity and up-regulated water-soluble carbohydrates (WSCs) would lead to better microbial efficiency in terms of improving silage amino acid profile (to be further explored), improved volatile fatty acids (VFAs) profile, decreased protein and amino acids degradation and NH3 production resulting in better silage overall quality and improved nutritive value. 

SKYEVIEW: In the current use of technologies to crack the lignin barrier with 'anaerobic tools', microbiology as it applies to anaerobic bioremediative processes (e. g. municipal activated waste sludge and marine ecohabitats) and the rumen pose scenarios where fibrolytics can be further explored. E-mail us if you wish to hear more about the latest in use of polymeric fragmentation with LC/MS (liquid chromatography/mass spectrophotometry) and dimerized fluorometric assays to isolate, identify and further characterize enzymes for fibrolysis of ligno-cellulose as feedstock for feed, food and energy and genomics to construct probes for hybridization studies to enumerate and identify microbial isolates with superior lignase activity and further genomics to resolve further "homologues" amongst enzyme activities. TFs (transcription factors) assays will further identify regulatory elements for lignase production. Enzymes are a cost-limiting technology to make manufacture of cellulosic ethanol a commercial proposition.  Polymeric fragmentation will require timed sampling and "distributional fingerprinting" of digested peaks on a homogeneous substrate of lignin (e. g. poplar).

SKYEVIEW: There is an indication from the published literature that anaerobic "ligninolytic" enzymes are beginning to be identified and characterized as to their mechanisms and kinetics to indicate as to how possibly effective they are.  The enzymes for facultatively anaerobic rumen fungi and strictly anaerobic fungi are etherases, esterases and dearomatization "ring" enzymes contributing to separating lignin from crystalline cellulose and leading to ring fissure.  There could also be a need for additional energy (ATP) for lignin oxidation contributing to its relative recalcitrance in degradation. 

SKYEVIEW: The application of lignozymes (or lignases as they are formally or systematically known, from their substrate lignin) that belong to the lignase type-II group (anaerobic) (type-I: aerobic from fungi in solid substrate fermentation(SSF); type-III: aerobic Cu3+-lacasses) are being investigated as to their rate or half-life of substrate breakdown for microbiotic spp. with lignases to be isolated, identified and characterized from soils or composts, municipal waste activated sludge (this shows most promise in terms of rate of depolymerization and mineralization of lignin backbones and ring fissure), from rumen microbiota of livestock including the carabao, Nili-Ravi or Murrah, and marine eco-habitats; the uses of type-II lignases [e. g. the depolymerases such as lyases, etherases, esterases and phenyl oxidases, and those enzymes that remove by dehydroxylation and demethoxylation of group substitutions on the aromatic rings of the phenyl propanoid subunits that constitute the building blocks and the 'larger networked chain of lignan', reduction of the benzene ring to the cyclohexane (2-hydroxycyclohexanecarboxyl Coenzyme A dehydrogenase) and then ring fissure leading eventually to mineralization to CO2 + H20, thus far having been investigated in lignan's breakdown] will have far-reaching implications in both aerobic (they are stable, it is presumed to atmospheric O2) and anaerobic applications competing on all fronts with both the fungi in SSF of feeds biomass as well as the practice of: 1) top dressing, 2) biocropping by sequestration until release when the cell dies upon harvesting or chewing by the grazing animal, 3) conventional ensilage to follow harvesting and 4) post-harvest technology such as release of sequestered enzymes with urea-ammoniation, yeast bagasse or steam explosion (SE)/sulfur dioxide (SO2) treatment.  There is much to be learned about the gains or improvements in production parameters with these new treatments and in combination with other treatments used for feeds post-harvest technology.

SKYEVIEW: Flores, et al. (1986), McGill U. in animal experiments with sheep probing methods to measure intestinal flows of amino acids using various dietary treatments as with fresh and ensiled alfalfa that had undergone degradation, and processing through the rumen stomach, demonstrated that digesta solids collected and analyzed for total amino acids (AA) showed significant differences in AA levels with diets that had degraded, reflecting dietary influences, despite microbial resynthesis to protein from microbial cell protein (MCP).  It was concluded that continuing studies were needed to support evidence that nitrogen (N) status of animals affect their intake, of the corresponding diet.  Here we reveal a point of controversy regarding Skye Blue's interests in studying the digestive tract as an endocrine organ that has a larger yet to be discovered role in 'mind-body'- axis theory (see: MEDBIOSE).  The duodenal digest samples collected were thrown out shortly after subsampling in 1983 without collection of the liquid supernatant, viz.: 1) further definition of the liquid phase of the duodenal and other parts of the digestive tract, 2) what mixing and propulsion means in terms of bulk flow and use of so-called solid / liquid-phase markers to correct for 'background' (random effects) and 3) use of dose-response concentrations of duodenal amino acids in the 'liquid' phase that might impact physiologically the digestive tract, viz. intake response or feedback loops to the CNS.    

SKYEVIEW: The method of re-entrant cannulation and sample collection and infusion with the s. intestines would be at points along the duodenum, jejunum, and ileum and involve measuring samples at each of these points for whatever parameters are required at these points [viz. free amino acids (FAAs)] at the duodenum, jejunum and ileum impacting that section of the digestive tract, or controlled studies measuring and confirming their impact by infusement of FAA mixtures at these points.  It is thus possible to corroborate findings from duodenal FAA flow measurements (viz. concentrations) and their possible impact on intake at the level of the digestive tract or s. intestines with controlled infusion data.

SKYEVIEW: In cell signaling, the proposed theory of 'OFF/ON switching' with nutritionals and/or their so-called "unique" bio/pharma where a dose-dependent relationship exists where a 'no response' state occurs below a lower threshold or an 'ON response' kicks in above this with the drug, to an upper asymptote or plateau, in which case drug toxicity may set in. This stipulates the existence of this switch along with the metabolism described for the pathways involved. In cases involving 'survival of the fitest' processes in metabolism, 'switching' could play a role as in the above e. g. where essential amino acid or nitrogen (N) status and well-being / health are involved in their absorption in the lower gut intestines. Another case   involving so-called "switching" may involve nutritionals and their metabolism, which as stated, above, would be a "unique" pharmaceutical approach. T2Diabetes presents an interesting scenario where one could speculate if intra-cellular (viz. in through cell membrane) cell signaling, if molecular "switching" (likely multiple) is involved, susceptability or genetic predisposition to glucose intolerance together with constant 'conditioning' and molecular events from elevated blood glucose levels and build up of fat depots as opposed to an alternative hypothesis of 'environmental' conditioning alone, whichever the case may be, in fat and lean body mass (LBM) response to insulin.  

Enzyme bioengineering for food/feed applications and use of probiotics in the rumen is on the drawing board. So is Bio-crop (Gen) (generic) development defined as a class of commercial plant crops with practical scope for both crops in feeds, food and bioenergy production. We also have an interest in biomedical instrumentation/device and manufacture for electrophoresis, functional food and applications and are being offered at this time for further collaboration. Bioenergy for economic and eco-friendly, sustainable development is a goal. (See: Global Association for Greening Community, at hum-molgen.de.)

Livestock byproduct feeding and processing are under development.  These include probiotics for feeds (e. g. tropical and temperate ensilage) including ground-breaking research on lignase enzymes currently at Skye Blue and ruminal probiotics including suicide plasmid - transposon technology and with fungal culture (reported from Australia/India partners).

The issue of probiotics in the rumen vis-a-vis other means of supplementation on low-quality feed byproducts such as pre-treatment and energy/protein byproduct concentrate feeding presents the following comparisons: 1) the use of boosting fibrolysis (e. g. with cellulases/hemicellulases and lignases) is of use especially with low planes of nutrition (e. g. with v. fibrous feeds or diets and water buffaloes who characteristically consume them), 2) the use of SCP in yeast fermentation and essential amino acid nitrogen (E.A.A.-N) and with probiotics with boosted branched-chain amino acids (br-A.A.s) can boost microbial cell protein (MCP) synthesis and 3) total nitrogen (TN) which includes non-protein-N (NPN, A.A.-N and other N) in  comparison presents no added benefit at certain levels with ammoniated straw and straw supplemented with protein concentrate, except, as has been hypothesized when the protein A.A.-N is protected which apparently effects more efficient uptake with greater efficiency of MCP synthesis and stimulation of cellulolytic activity and fibre digestion in the rumen.

The means of increasing digestibility, and especially, fibre digestibility would be first to remove the first barrier of enzymatic attack on fibre, lignin, either by: decreasing lignin content genetically as has been done with certain varieties of forage, physically dissociating bonds between lignin and fibre (specifically hemicellulosic moieties) by steam explosion (elevated moist temperature and pressure), ammoniation pre-treatment of fibrous residues, bio-bleaching with aerobic type-III lignases or lacasses, as they are called, and finally use of anaerobic lignases (there are outstanding issues of the level of enzyme production and the efficiency or Kcat of the enzyme) from rumen stomachs which participate in digestion of fibrous ingested feeds and from human waste municipal collection sites.  After the first action here there is then the issue of the addition of the cellulase gene as with genetically modified (GM) processed feeds as with: temperate silage, yeast bagasse fermentation and compounding and ammoniation with symbiotic species. (Solid-substrate fermentation (SSF) using Basidiomycetes might require genetically improved aerobic lignases that act quicker to depolymerize lignin so much as to spare organic matter loss due to fungal spp.) Freeing fibre from lignin by physical treatment or decreasing the lignin content by about half has led to a 15-20% increase in digestibility points and it is only estimable at this point what cellulase (and other fibrolytic enzymes) would do to further improve performance.

Bio-crops (Gen) varieties still have not been produced for markets and has at this time been regulated for use only with pesticide control and herbicide tolerance although it also has been  proposed that widespread research activity on boosting sugars beneficial to microbial digestion and other prebiotic effects (e. g. anti-protozoal forage, low-protease forages wilted when harvested and ionophoric peptides coded feeds) with animals be produced with forage spp. using both marker identification and mapping to important gene determinants and used in molecular assisted selection (MAS) or breeding and genetic modification (GM).

An area that has now reached considerable attention with hopes that a robust crop that is safe, pest resistant, environmentally adaptable, possesses good seed nutrient composition and has good heritability can be developed.  The seed is already a reality and shows no adverse pleiotropic effects (due to possible imbalance of metabolic fluxes) on seed development.  The high free threonine (Thr) soybean developing seeds was developed by introducing bacterial XbAK [aspartate kinase in the amino acid branched pathways with Thr, Lysine (Lys), Methionine (Met) and Isoleucine (Ile)] gene variants that was site-directed mutated with the replacement of Thr-359 for Ile and Glutamic acid-257 (Glu-257) for Lys showing less allosteric feedback inhibition but no changes in other kinetic parameters except a lower KmATP.  The alleles called XbAK-T359I and XbAK-E257K with the use of high speed genomics and tagging and gene markers where introduced into seeds using seed-specific promoters 7Sa' or USP997 and a chloroplast plastid targetting sequence CTP1.  The bacterial gene XbAK was recovered by HPLC.

There is an outstanding issue that is to be addressed in future likewise regarding essential amino acid with food consumption in food/feed sources that supply commensurate EAA content in addition to increasing caloric intake in food production which, in actual cases at this time, would be: Lys and Trytophane (Trp) in maize, Met and Thr in soybeans, Met, Cysteine (Cys) and Ile in potatoes and Lys and Thr in rice.

Genetically modified (GM) and non-GM feed processing and cropping for small farms in tropical developing countries is being called of at this time with the spectre of overpopulation and pressure to produce more of what is already stretched food resources such as with India.

The use of alkali was earlier proposed to treat ligno-cellulose in fibre feed residues but lost acceptance due to its lower cost-effectiveness compared to feeding supplements (e. g. protein and energy concentrates from farming, co-op and industrial feeds and food processing).  High-tech or GM technologies with crops (lowering lignin content and boosting water-soluble carbohydrate (WSC) and non-structural carbohydrate (NSC) (that are shorter oligomers and ferment faster resulting in more rapid, efficient energy yield) has proven to be comparable in nutritive value compared to supplement feeding. 

It has been proposed that GM feed processing together with GM crops might present new approaches to improved feeding practices including the ammoniation with GM symbionts of GM low-ligin forages and their residue byproducts which would be more cost-effective to another alternative of feeding energy supplements and in addition supply the requirement for crude protein-N for microbial fermentation to be used with GM-feeds with bypass or escape protein.  Also, introduction of WSC and NSC in the GM biocrop would improve microbial efficiency and yield on the energy in biomass fermented further, as was mentioned. 

It is expected that it would be possible to approach the problem of boosting chorophyll a & b content and the prospect of boosting production of biomass in crops for feed and biofuel feedstock such as has been proposed with high efficiency sugarcane and sorghum species.  The multiple trait-linked expression of chlorophyll production and its overproduction will prove a daunting challenge to scientists including possible pleiotropic effects. The photosynthetic action of chlorophyll is believed like energy metabolic pathways to be boosted in turnover when genetically expressed.  Further to this are the phototropic pigments in photosynthetic organisms like algae which have a greater efficiency in photo conversion which can be architecturally (i. e. structurally) stacked to complement plant photosynthetic activity.

Growth areas in plant-based products include energy biofuels [e. g. bioethanol, n-butanol (ABE), biogas (CH4) and biodiesel and phyto-olefins].  Also, there are biofine resources from biomass sources including paints, solvents, adhesives, resins and finishes, construction and packaging material including those from polymeric resins, plastics and polysynthetics for clothing, outerwear for fashion, recreation or sportswear and a vast area of other environmental applications.

In lastest developments with algal biomass production for cosmetics, pharma, feed, food and bioenergy (oil) applications, photobioreactors that maintain temperature with mixing/heating with power plants (e. g.  CH4), a branched design which offers maximum light exposure with use of specialized plastics preventing biofilm formation and cost-effective use of CO2 and nutrients including waste water and on-going selection of fast-growing spp, will allow practical delivery of systems several hundred hectares in area.  Areas that have been used for their ideal weather conditions are New Mexico U.S.A. and Queensland Australia.

In studies in the Philippines there could be cultural, socio-economic and technology transfer advantages for the production of increased dairy lactation from the increased practice of feeding fibrous residues, byproduct generation of whey from cheese dairy production and its use further in biogas production by the rapid process natural gas (RPNG) and biodiesel production (methyl esters converted from triglyceride or lipid) from photosynthetic algae (and soon also to be developed from seaweed in seawater field tanks) in tandem with dual sugar fermentation to n-butanol (acetone, butanol, ethanol)(ABE).

The use of wet fermentation versus solid-state fermentation as a point of reference has identified rumen or silage fermentation in addition to biopharma and biofuel fermentation in the wet category and feed treatment with fungal culture (e, g. Basidiomycetes) in the 'dry' category.  There is a breakthrough with the latter with the prospect of using lignases to a limited extent to 'top dress' fungal fermentative lignocellulolysis of fibre making energy more available and making available their natural detoxifying biofermentative action.  Feed residue feeding practices in the Philippines with water buffalo with high producers of caramilk would make this an ideal area to make it more practicable and a score a breakthrough in caramilk production in the country.

A study particular to Skye Blue and under publication (see Flores et al.) is the role of simple sugars on rumen fermentation and volatile fatty acid (VFA) production and degradation of proteins and their rumen lability and contribution to proteinogenesis microbially.  There is data available that relates these two factors to proteinogenic efficiency as possible candidates for further research.

An area we are involved with research at the moment with ensilage (tropical and temperate) and rumen digestion and its manipulation is biotechnology applied to ensilage and probiotics in rumen digestion. In the tropics haymaking would be the method of choice. But also in the tropics ensilage, where there is a marked wet season (e. g. China and Australia).  Also limited forage supplies during the dry season is making ensilage a practice to consider of choice for throughout the year. The meteorological seasons for planting, byproduct production and use, C4 output or yield and potential to treat fibre and improved ensilage practices would make world-wide production of crops for ensilage of increasing choice. The use of fibrolytics to increase the sugar availability should result in decreased NH3-N (nitrogen) and increased VFAs (volatile fatty acids) production. Preliminary data shows that osmotic pressure restriction and protection of nitrogen (N) would be called for with tropical ensilage. Transport processes of amino acids (AAs) may be limiting the efficiency of MCP (microbial) synthesis. Decreased NH3-N and increased VFAs would be consistent with increased N utilization for MCP synthesis and increased output of VFAs from increased availability of sugars and carbohydrates from fibrolytic enzymes. Future work with ligninolytics will be a major breakthrough with fibrolysis in feeds and rumen digestion. The annexation of lignases with ammoniation of straw, is an application with feeds pre-treatment and use of this biofermentation process. Yeast and fungal probiotics are the only probiotics that sucessfully persist in the rumen and have demonstrated benefits to rumen digestion and are commercially viable propositions. RNAi small molecular techniques with low energy of maintenance conjugative suicide plasmid - transposons with operon elements for controlling enzymes (viz. cellulases, hemicellulases, pectinases and lignases) are possible applications. There are no known studies of operon control mechanisms/modeling with rumen microbial species. It will be assumed, for now, that a lac operon-like model where cellobiose together with other low molecular weight (LMW) mRNA product(s) acts as an indicator for fibre digestion and acts on the operator to prevent expression of cellulase allowing for RNAi to be introduced in microbial DNA and blocking LMW products from expression acting to cause 'run-a-way' production of fibrolytic enzyme(s).

SKYEVIEW:The continuing story of inflammation and its role with fructan and Vit D in heart disease, diabetesT2 and colo-rectal cancer has now focused in the Philippines in their commonly held spp. Annona muricata Linn (guayabano, in the common dialect) leaf or tea and fruit extract that have demonstrated to be anti-inflammatory in animal studies and should be further investigated for active substances (viz. except toxins, alkaloids) such as annonaceous acetogenins that may help in reducing insulin resistance, atherosclerotic plaques and inflammation in the lower bowel leading to colo-rectal cancer.  It should be added that guayabano extract kills cancer cells and also indirectly leads to increased insulin production in T2 diabetic cases.

SKYEVIEW: What wonders Filipino phytopharm can offer from our plethora from forests, orchards, farms and fields and its native flora.  We'll be sure to work away as to what active substances (e. g. in this case, annonaceous acetogenins) have been thus researched in our much loved and luscious guayabano fruit - and their 'tea leaves', that controls the inflammation response, at Skye Blue, as has similarly been found with fructan and Vit D and what perspectives this offers in terms of small organic molecules and drugs in molecular medicine.






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