Biotechnology, Bioinformatics & Genomic Technology Research and Development
Designing and Developing Artificial Intelligence, Deep Learning and Machine Learning for Medical Research, Healthcare, Health Information Technology - HIT / HealthIT & Medical Technology - MedTech
HubBucket Biotechnology ("HubBioTech") is a Research and Development - R&D department within HubBucket, Inc. ("HubBucket") that focuses on the design and development of technology for Genomics Research and Development, coupled with the design and development of other Medical Research technology.
However you define bioinformatics, as broadly or narrowly as you wish, it fundamentally enables the modern day researcher to handle and analyze large and complex data – the big data challenge – an essential part of understanding biology.
HubBucket Biotechnology ("HubBioTech") focuses on delivering robust, high quality and relevant bioinformatics services for life science researchers to analyze and manage large-scale datasets.
We offer our clients a range of professional services – from contract research, project design and analysis, scientific software development, to designing, deploying and refining the high performance IT infrastructure that is required to support life science informatics.
Our computational biology support ranges from experimental design, data capture and mining through to NGS, proteomic and metabolomic analyses. We are also expert in cross-domain integration with clinical data.
As a team, we are committed to operating ethically, with integrity and respect at all times. We believe that open communication, flexibility and honesty are the keys to successful customer engagement.
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Modern biotechnology provides breakthrough products and technologies to combat debilitating and rare diseases, reduce our environmental footprint, feed the hungry, use less and cleaner energy, and have safer, cleaner and more efficient industrial manufacturing processes.
Currently, there are more than 250 biotechnology health care products and vaccines available to patients, many for previously untreatable diseases. More than 13.3 million farmers around the world use agricultural biotechnology to increase yields, prevent damage from insects and pests and reduce farming's impact on the environment. And more than 50 biorefineries are being built across North America to test and refine technologies to produce biofuels and chemicals from renewable biomass, which can help reduce greenhouse gas emissions.
Recent advances in biotechnology are helping us prepare for and meet society’s most pressing challenges. Here's how
Heal the World
Biotech is helping to heal the world by harnessing nature's own toolbox and using our own genetic makeup to heal and guide lines of research by:
- Reducing rates of infectious disease;
- Saving millions of children's lives;
- Changing the odds of serious, life-threatening conditions affecting millions around the world;
- Tailoring treatments to individuals to minimize health risks and side effects;
- Creating more precise tools for disease detection; and
- Combating serious illnesses and everyday threats confronting the developing world.
Fuel the World
Biotech uses biological processes such as fermentation and harnesses biocatalysts such as enzymes, yeast, and other microbes to become microscopic manufacturing plants. Biotech is helping to fuel the world by:
- Streamlining the steps in chemical manufacturing processes by 80% or more;
- Lowering the temperature for cleaning clothes and potentially saving $4.1 billion annually;
- Improving manufacturing process efficiency to save 50% or more on operating costs;
- Reducing use of and reliance on petrochemicals;
- Using biofuels to cut greenhouse gas emissions by 52% or more;
- Decreasing water usage and waste generation; and
- Tapping into the full potential of traditional biomass waste products.
Feed the World
Biotech improves crop insect resistance, enhances crop herbicide tolerance and facilitates the use of more environmentally sustainable farming practices. Biotech is helping to feed the world by:
- Generating higher crop yields with fewer inputs;
- Lowering volumes of agricultural chemicals required by crops-limiting the run-off of these products into the environment;
- Using biotech crops that need fewer applications of pesticides and that allow farmers to reduce tilling farmland;
- Developing crops with enhanced nutrition profiles that solve vitamin and nutrient deficiencies;
- Producing foods free of allergens and toxins such as mycotoxin; and
- Improving food and crop oil content to help improve cardiovascular health.
HubBucket Biotechnology ("HubBioTech") is a research and development - R&D department within HubBucket, Inc. ("HubBucket"), that focuses on the design and development of Biotechnology, Bioinformatics, etc., technology for:
- Health Information Technology - HealthIT / HIT
- Medical Technology - MedTech
- Medical Research Technology
We design and develop technology to assist Medical Researchers, Medical Doctors and Healthcare Providers find cures to diseases such as Cancer, Autoimmune Diseases, Alzheimer's Disease, Addison's Disease, Parkinson's Disease, Diabetes, etc., and to help Medical Doctors and Healthcare Providers treat their patients and mange Population Healthcare Management.
We design and develop:
- Artificial Intelligence - AI
- Machine Learning - ML
- Deep Learning - DL
- Artificial Neural Networks - ANN
- Natural Language Processing - NLP
- Natural Language Understanding - NLU
- Neural Machine Translation - NMT
- Machine Vision - MV
- Computer Vision - CV
- Electronic Healthcare Records - EHR
- Electronic Medical Records - EMR
- Medical Imaging applications and systems
- Mobile Healthcare Applications - Mobile Apps
- Mobile Medical Applications - Mobile Apps
- Remote Monitoring applications and systems
- AND A LOT MORE
HubBioTech explores the different aspects of bioinformation systems, from theoretical approaches to modeling different phenomena in life sciences, to information technologies necessary for analysis and understanding huge amount of data generated, to application of Computer Science (CS) and informatics in the domain of precision medicine, finding new remedies against debilitating diseases (like cancer and neurodegeneration) and drug development.
In this area, we focus on three main research fields including (but not limited to) the following topics:
Theoretical Approaches to BioInformation Systems:
- Structure and function of DNA, RNA and proteins
- Gene expression and the genetic code
- Neurons and cognition
- Biological networks
Bioinformatics and Data Mining for OMICs Data:
- Data mining methods, algorithms, and applications in life sciences and precision medicine
- Big data and data science
- Data analytics, pattern recognition and machine learning in data analysis
- Software and tools in genomics, proteomics, metabolomics, transcriptomics, epigenomics, etc.
- Sequence analysis
- Predictive Models for OMICs data
- Bioinformatics databases and algorithms
Biomedical Informatics will focus on information applied to or studied in the context of biomedicine:
- Translational Bioinformatics
- Disease Models & Epidemiology
- Predictive Modeling and Analytics in Healthcare
- Biomedical Imaging and Data Visualization
- Biomedical/Health database integration and management
- Biomedical data/text mining
Biotechnology is the use of living systems and organisms to develop or make products, or "any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use" (UN Convention on Biological Diversity, Art. 2). Depending on the tools and applications, it often overlaps with the (related) fields of bioengineering, biomedical engineering, biomanufacturing, molecular engineering, etc.
For thousands of years, humankind has used biotechnology in agriculture, food production, and medicine. The term is largely believed to have been coined in 1919 by Hungarian engineer Károly Ereky. In the late 20th and early 21st centuries, biotechnology has expanded to include new and diverse sciences such as genomics, recombinant gene techniques, applied immunology, and development of pharmaceutical therapies and diagnostic tests.
The wide concept of "biotech" or "biotechnology" encompasses a wide range of procedures for modifying living organisms according to human purposes, going back to domestication of animals, cultivation of the plants, and "improvements" to these through breeding programs that employ artificial selection and hybridization. Modern usage also includes genetic engineering as well as cell and tissue culture technologies. The American Chemical Society defines biotechnology as the application of biological organisms, systems, or processes by various industries to learning about the science of life and the improvement of the value of materials and organisms such as pharmaceuticals, crops, and livestock. As per European Federation of Biotechnology, biotechnology is the integration of natural science and organisms, cells, parts thereof, and molecular analogues for products and services. Biotechnology also writes on the pure biological sciences (animal cell culture, biochemistry, cell biology, embryology, genetics, microbiology, and molecular biology). In many instances, it is also dependent on knowledge and methods from outside the sphere of biology including:
- bioinformatics, a new brand of computer science
- bioprocess engineering
- chemical engineering
Conversely, modern biological sciences (including even concepts such as molecular ecology) are intimately entwined and heavily dependent on the methods developed through biotechnology and what is commonly thought of as the life sciences industry. Biotechnology is the research and development in the laboratory using bioinformatics for exploration, extraction, exploitation and production from any living organisms and any source of biomass by means of biochemical engineering where high value-added products could be planned (reproduced by biosynthesis, for example), forecasted, formulated, developed, manufactured, and marketed for the purpose of sustainable operations (for the return from bottomless initial investment on R & D) and gaining durable patents rights (for exclusives rights for sales, and prior to this to receive national and international approval from the results on animal experiment and human experiment, especially on the pharmaceutical branch of biotechnology to prevent any undetected side-effects or safety concerns by using the products).
By contrast, bioengineering is generally thought of as a related field that more heavily emphasizes higher systems approaches (not necessarily the altering or using of biological materials directly) for interfacing with and utilizing living things. Bioengineering is the application of the principles of engineering and natural sciences to tissues, cells and molecules. This can be considered as the use of knowledge from working with and manipulating biology to achieve a result that can improve functions in plants and animals. Relatedly, biomedical engineering is an overlapping field that often draws upon and applies biotechnology (by various definitions), especially in certain sub-fields of biomedical and/or chemical engineering such as tissue engineering, biopharmaceutical engineering, and genetic engineering.
Although not normally what first comes to mind, many forms of human-derived agriculture clearly fit the broad definition of "'utilizing a biotechnological system to make products". Indeed, the cultivation of plants may be viewed as the earliest biotechnological enterprise.
Agriculture has been theorized to have become the dominant way of producing food since the Neolithic Revolution. Through early biotechnology, the earliest farmers selected and bred the best suited crops, having the highest yields, to produce enough food to support a growing population. As crops and fields became increasingly large and difficult to maintain, it was discovered that specific organisms and their by-products could effectively fertilize, restore nitrogen, and control pests. Throughout the history of agriculture, farmers have inadvertently altered the genetics of their crops through introducing them to new environments and breeding them with other plants — one of the first forms of biotechnology.
These processes also were included in early fermentation of beer. These processes were introduced in early Mesopotamia, Egypt, China and India, and still use the same basic biological methods. In brewing, malted grains (containing enzymes) convert starch from grains into sugar and then adding specific yeasts to produce beer. In this process, carbohydrates in the grains were broken down into alcohols such as ethanol. Later other cultures produced the process of lactic acid fermentation which allowed the fermentation and preservation of other forms of food, such as soy sauce. Fermentation was also used in this time period to produce leavened bread. Although the process of fermentation was not fully understood until Louis Pasteur's work in 1857, it is still the first use of biotechnology to convert a food source into another form.
Before the time of Charles Darwin's work and life, animal and plant scientists had already used selective breeding. Darwin added to that body of work with his scientific observations about the ability of science to change species. These accounts contributed to Darwin's theory of natural selection.
For thousands of years, humans have used selective breeding to improve production of crops and livestock to use them for food. In selective breeding, organisms with desirable characteristics are mated to produce offspring with the same characteristics. For example, this technique was used with corn to produce the largest and sweetest crops.
In the early twentieth century scientists gained a greater understanding of microbiology and explored ways of manufacturing specific products. In 1917, Chaim Weizmann first used a pure microbiological culture in an industrial process, that of manufacturing corn starch using Clostridium acetobutylicum, to produce acetone, which the United Kingdom desperately needed to manufacture explosives during World War I.
Biotechnology has also led to the development of antibiotics. In 1928, Alexander Fleming discovered the mold Penicillium. His work led to the purification of the antibiotic compound formed by the mold by Howard Florey, Ernst Boris Chain and Norman Heatley – to form what we today know as penicillin. In 1940, penicillin became available for medicinal use to treat bacterial infections in humans.
The field of modern biotechnology is generally thought of as having been born in 1971 when Paul Berg's (Stanford) experiments in gene splicing had early success. Herbert W. Boyer (Univ. Calif. at San Francisco) and Stanley N. Cohen (Stanford) significantly advanced the new technology in 1972 by transferring genetic material into a bacterium, such that the imported material would be reproduced. The commercial viability of a biotechnology industry was significantly expanded on June 16, 1980, when the United States Supreme Court ruled that a genetically modified microorganism could be patented in the case of Diamond v. Chakrabarty. Indian-born Ananda Chakrabarty, working for General Electric, had modified a bacterium (of the Pseudomonas genus) capable of breaking down crude oil, which he proposed to use in treating oil spills. (Chakrabarty's work did not involve gene manipulation but rather the transfer of entire organelles between strains of the Pseudomonas bacterium.
Revenue in the industry is expected to grow by 12.9% in 2008. Another factor influencing the biotechnology sector's success is improved intellectual property rights legislation—and enforcement—worldwide, as well as strengthened demand for medical and pharmaceutical products to cope with an ageing, and ailing, U.S. population.
Rising demand for biofuels is expected to be good news for the biotechnology sector, with the Department of Energy estimating ethanol usage could reduce U.S. petroleum-derived fuel consumption by up to 30% by 2030. The biotechnology sector has allowed the U.S. farming industry to rapidly increase its supply of corn and soybeans—the main inputs into biofuels—by developing genetically modified seeds which are resistant to pests and drought. By boosting farm productivity, biotechnology plays a crucial role in ensuring that biofuel production targets are met.
Biotechnology has applications in four major industrial areas, including health care (medical), crop production and agriculture, non food (industrial) uses of crops and other products (e.g. biodegradable plastics, vegetable oil, biofuels), and environmental uses.
For example, one application of biotechnology is the directed use of organisms for the manufacture of organic products (examples include beer and milk products). Another example is using naturally present bacteria by the mining industry in bioleaching. Biotechnology is also used to recycle, treat waste, clean up sites contaminated by industrial activities (bioremediation), and also to produce biological weapons.
A series of derived terms have been coined to identify several branches of biotechnology; for example:
- Bioinformatics is an interdisciplinary field which addresses biological problems using computational techniques, and makes the rapid organization as well as analysis of biological data possible. The field may also be referred to as computational biology, and can be defined as, "conceptualizing biology in terms of molecules and then applying informatics techniques to understand and organize the information associated with these molecules, on a large scale." Bioinformatics plays a key role in various areas, such as functional genomics, structural genomics, and proteomics, and forms a key component in the biotechnology and pharmaceutical sector.
- Blue biotechnology is a term that has been used to describe the marine and aquatic applications of biotechnology, but its use is relatively rare.
- Green biotechnology is biotechnology applied to agricultural processes. An example would be the selection and domestication of plants via micropropagation. Another example is the designing of transgenic plants to grow under specific environments in the presence (or absence) of chemicals. One hope is that green biotechnology might produce more environmentally friendly solutions than traditional industrial agriculture. An example of this is the engineering of a plant to express a pesticide, thereby ending the need of external application of pesticides. An example of this would be Bt corn. Whether or not green biotechnology products such as this are ultimately more environmentally friendly is a topic of considerable debate.
- Red biotechnology is applied to medical processes. Some examples are the designing of organisms to produce antibiotics, and the engineering of genetic cures through genetic manipulation.
- White biotechnology, also known as industrial biotechnology, is biotechnology applied to industrial processes. An example is the designing of an organism to produce a useful chemical. Another example is the using of enzymes as industrial catalysts to either produce valuable chemicals or destroy hazardous/polluting chemicals. White biotechnology tends to consume less in resources than traditional processes used to produce industrial goods.
The investment and economic output of all of these types of applied biotechnologies is termed as "bioeconomy".
In medicine, modern biotechnology finds applications in areas such as pharmaceutical drug discovery and production, pharmacogenomics, and genetic testing (or genetic screening).
Pharmacogenomics (a combination of pharmacology and genomics) is the technology that analyses how genetic makeup affects an individual's response to drugs. It deals with the influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms with a drug's efficacy or toxicity. By doing so, pharmacogenomics aims to develop rational means to optimize drug therapy, with respect to the patients' genotype, to ensure maximum efficacy with minimal adverse effects. Such approaches promise the advent of "personalized medicine"; in which drugs and drug combinations are optimized for each individual's unique genetic makeup.
Biotechnology has contributed to the discovery and manufacturing of traditional small molecule pharmaceutical drugs as well as drugs that are the product of biotechnology – biopharmaceutics. Modern biotechnology can be used to manufacture existing medicines relatively easily and cheaply. The first genetically engineered products were medicines designed to treat human diseases. To cite one example, in 1978 Genentech developed synthetic humanized insulin by joining its gene with a plasmid vector inserted into the bacterium Escherichia coli. Insulin, widely used for the treatment of diabetes, was previously extracted from the pancreas of abattoir animals (cattle and/or pigs). The resulting genetically engineered bacterium enabled the production of vast quantities of synthetic human insulin at relatively low cost. Biotechnology has also enabled emerging therapeutics like gene therapy. The application of biotechnology to basic science (for example through the Human Genome Project) has also dramatically improved our understanding of biology and as our scientific knowledge of normal and disease biology has increased, our ability to develop new medicines to treat previously untreatable diseases has increased as well.
Genetic testing allows the genetic diagnosis of vulnerabilities to inherited diseases, and can also be used to determine a child's parentage (genetic mother and father) or in general a person's ancestry. In addition to studying chromosomes to the level of individual genes, genetic testing in a broader sense includes biochemical tests for the possible presence of genetic diseases, or mutant forms of genes associated with increased risk of developing genetic disorders. Genetic testing identifies changes in chromosomes, genes, or proteins. Most of the time, testing is used to find changes that are associated with inherited disorders. The results of a genetic test can confirm or rule out a suspected genetic condition or help determine a person's chance of developing or passing on a genetic disorder. As of 2011 several hundred genetic tests were in use. Since genetic testing may open up ethical or psychological problems, genetic testing is often accompanied by genetic counseling.
Genetically modified crops ("GM crops", or "biotech crops") are plants used in agriculture, the DNA of which has been modified with genetic engineering techniques. In most cases the aim is to introduce a new trait to the plant which does not occur naturally in the species.
Examples in food crops include resistance to certain pests, diseases, stressful environmental conditions, resistance to chemical treatments (e.g. resistance to a herbicide), reduction of spoilage, or improving the nutrient profile of the crop. Examples in non-food crops include production of pharmaceutical agents, biofuels, and other industrially useful goods, as well as for bioremediation.
Farmers have widely adopted GM technology. Between 1996 and 2011, the total surface area of land cultivated with GM crops had increased by a factor of 94, from 17,000 square kilometers (4,200,000 acres) to 1,600,000 km2 (395 million acres). 10% of the world's crop lands were planted with GM crops in 2010. As of 2011, 11 different transgenic crops were grown commercially on 395 million acres (160 million hectares) in 29 countries such as the USA, Brazil, Argentina, India, Canada, China, Paraguay, Pakistan, South Africa, Uruguay, Bolivia, Australia, Philippines, Myanmar, Burkina Faso, Mexico and Spain.
Genetically modified foods are foods produced from organisms that have had specific changes introduced into their DNA with the methods of genetic engineering. These techniques have allowed for the introduction of new crop traits as well as a far greater control over a food's genetic structure than previously afforded by methods such as selective breeding and mutation breeding. Commercial sale of genetically modified foods began in 1994, when Calgene first marketed its Flavr Savr delayed ripening tomato. To date most genetic modification of foods have primarily focused on cash crops in high demand by farmers such as soybean, corn, canola, and cotton seed oil. These have been engineered for resistance to pathogens and herbicides and better nutrient profiles. GM livestock have also been experimentally developed, although as of November 2013 none are currently on the market.
There is a scientific consensus that currently available food derived from GM crops poses no greater risk to human health than conventional food, but that each GM food needs to be tested on a case-by-case basis before introduction. Nonetheless, members of the public are much less likely than scientists to perceive GM foods as safe. The legal and regulatory status of GM foods varies by country, with some nations banning or restricting them, and others permitting them with widely differing degrees of regulation.
GM crops also provide a number of ecological benefits, if not used in excess. However, opponents have objected to GM crops per se on several grounds, including environmental concerns, whether food produced from GM crops is safe, whether GM crops are needed to address the world's food needs, and economic concerns raised by the fact these organisms are subject to intellectual property law.
Industrial biotechnology (known mainly in Europe as white biotechnology) is the application of biotechnology for industrial purposes, including industrial fermentation. It includes the practice of using cells such as micro-organisms, or components of cells like enzymes, to generate industrially useful products in sectors such as chemicals, food and feed, detergents, paper and pulp, textiles and biofuels. In doing so, biotechnology uses renewable raw materials and may contribute to lowering greenhouse gas emissions and moving away from a petrochemical-based economy.
The environment can be affected by biotechnologies, both positively and adversely. Vallero and others have argued that the difference between beneficial biotechnology (e.g. bioremediation to clean up an oil spill or hazard chemical leak) versus the adverse effects stemming from biotechnological enterprises (e.g. flow of genetic material from transgenic organisms into wild strains) can be seen as applications and implications, respectively. Cleaning up environmental wastes is an example of an application of environmental biotechnology; whereas loss of biodiversity or loss of containment of a harmful microbe are examples of environmental implications of biotechnology.
The regulation of genetic engineering concerns approaches taken by governments to assess and manage the risks associated with the use of genetic engineering technology, and the development and release of genetically modified organisms (GMO), including genetically modified crops and genetically modified fish. There are differences in the regulation of GMOs between countries, with some of the most marked differences occurring between the USA and Europe. Regulation varies in a given country depending on the intended use of the products of the genetic engineering. For example, a crop not intended for food use is generally not reviewed by authorities responsible for food safety. The European Union differentiates between approval for cultivation within the EU and approval for import and processing. While only a few GMOs have been approved for cultivation in the EU a number of GMOs have been approved for import and processing. The cultivation of GMOs has triggered a debate about coexistence of GM and non GM crops. Depending on the coexistence regulations incentives for cultivation of GM crops differ.
In 1988, after prompting from the United States Congress, the National Institute of General Medical Sciences (National Institutes of Health) (NIGMS) instituted a funding mechanism for biotechnology training. Universities nationwide compete for these funds to establish Biotechnology Training Programs (BTPs). Each successful application is generally funded for five years then must be competitively renewed. Graduate students in turn compete for acceptance into a BTP; if accepted, then stipend, tuition and health insurance support is provided for two or three years during the course of their Ph.D. thesis work. Nineteen institutions offer NIGMS supported BTPs. Biotechnology training is also offered at the undergraduate level and in community colleges.
SOURCE URL: https://en.wikipedia.org/wiki/Biotechnology
Genomics refers to the study of the entire genome of an organism (whereas genetics refers to the study of a particular gene). The human genome is the complete set of genetic information for humans and includes both protein-coding genes and non-coding regions.
Research into the field of genomics allows us to build a better understanding of the role genes play in our health and disease. When applied to cancer diagnostic development, genomics has the potential to provide new, more accurate information about patient risk that can change the way that cancer patients are managed.
Genomic testing can help physicians and their patients make more informed decisions about management and treatment by arming them with more accurate, personalized information about the course of a patient’s disease. Genomic tests have the potential to support treatment decisions by identifying who can safely avoid additional treatment, and determining who may benefit from earlier, more aggressive therapeutic options.
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