Research and development of biological hydrogen production have expanded significantly in the past decade. Production of renewable hydrogen from agricultural, forestry, or other organic waste streams offers the possibility to contribute to hydrogen production capacity with no net, or at least with lower, greenhouse gas emissions. Significant improvements in the volumetric or molar yields of hydrogen production have been accomplished through genetic engineering of hydrogen synthesizing microorganisms. Although no commercial scale renewable biohydrogen production facilities are currently in operation, a few pilot scale systems have been demonstrated successfully, and while industrial scale production of biohydrogen still faces a number of technical and economic barriers, understanding the patent landscape is an important step in developing a viable commercialization strategy. In this paper, we review patents filed on biological hydrogen production. Patents on biohydrogen production from both the Canadian and American Patents databases were classified into three main groups: (1) patents for biological hydrogen by direct photolysis; (2) patents for biological hydrogen by dark fermentation; and (3) patents for process engineering for biological hydrogen production.
Directed evolution shortcuts million-year-scale natural evolution in a matter of weeks and generates tens of millions of sequence variants in a single test tube. A team of researchers used random DNA flanked by homologous sequences for in vivo homologous recombination, known as multiplex automated genome engineering (MAGE) to select the most active gene variants. They also adopted this approach to replace hundreds of stop codons in the E. coli genome, showing potential for genome-wide engineering. The blank codon created was harnessed to enlarge the amino acid alphabet, and unnatural amino acid has been incorporated to polypeptides. In phage-assisted continuous evolution (PACE), the target activity was linked to the expression of a protein required for the production of infectious phage, and researchers obtained activities with novel affinities to T3 promoter, ATP, etc. In vitro recombination enables the generation of massive number of artificial lives of potential values. Random combinatorial DNA approach has also been harnessed to construct G-H loop sequences of type O FMDV VP1 gene, and 100 novel radical sequence variants were obtained in a single experiment, which paves the way for the future investigations on the potential development of a polyvalent vaccine to cope with rapid viral variations. The enormous combinatorial diversity of these methods conferred high mutation rates at either full length genes or targeted regions unmatched by natural evolution or previous directed evolution methods. Interactions of mutations or epistasis may have generated beneficial phenotypes from neutral and deleterious mutations. Selection for desired phenotypes may create sequence variants that might never occur in evolution. Accelerated molecular evolution methods, capitalized on random DNA strings, continuous evolution, unnatural amino acids or in vitro recombination, provide infinite opportunities for research, industrial and medical applications.
C-reactive protein (CRP) is a homopentameric oligoprotein composed of monomeric subunits that are about 21 kD each. The form of detectable native CRP in validated assays was developed in 2007 and from that time has been considered as an excellent biomarker for peripheral artery disease and/or atherosclerosis, as well as a cardiovascular disease marker for risk prediction. The improvements in the detection of CRP levels could predict significantly the population that have increased risk of stroke being the modulation of CRP levels as a therapeutical outcome for prevention of cardiovascular diseases. Nowadays antibodies that specifically bind CRP, as monoclonal anti-CRP antibodies, are available from commercial sources. Aptamers are biomolecules conformed principally by RNA or DNA, able to adopt secondary structures that can bind to epitopes from oligopeptides or complete proteins. The sensitivity and accuracy of aptamers has let to consider them as more efficient to identify proteins than just antibodies. These properties have become the base for testing these molecules for different uses. A battery of patented aptamers has been developed for detecting and/or measuring CRP. In this sense, aptamers against CRP (CRP-apt) would help to modulate CRP physiological actions at systemic, tissue, cellular and molecular levels by using appropriate experimental designs. This kind of studies would lead to fully understand which systems are regulated by the protein, what disturbances are produced if the CRP is missing or overexpressed. Finally, we hallmark other applications of CRP in terms of patents for both basic and applied research.
With dwindling fossil oil resources and increased economic growth of many developing countries due to globalization, energy driven from an alternative source such as bio-energy in a sustainable fashion is the need of the hour. However, production of energy from biological source is relatively expensive due to low starch and sugar contents of bioenergy plants leading to lower oil yield and reduced quality along with lower conversion efficiency of feedstock. In this context genetic improvement of bio-energy plants offers a viable solution. In this manuscript, we reviewed the current status of functional genomics studies and related patent activities in bio-energy plants. Currently, genomes of considerable bio-energy plants have been sequenced or are in progress and also large amount of expression sequence tags (EST) or cDNA sequences are available from them. These studies provide fundamental data for more reliable genome annotation and as a result, several genomes have been annotated in a genome-wide level. In addition to this effort, various mutagenesis tools have also been employed to develop mutant populations for characterization of genes that are involved in bioenergy quantitative traits. With the progress made on functional genomics of important bio-energy plants, more patents were filed with a significant number of them focusing on genes and DNA sequences which may involve in improvement of bio-energy traits including higher yield and quality of starch, sugar and oil. We also believe that these studies will lead to the generation of genetically altered plants with improved tolerance to various abiotic and biotic stresses.
Burning fossil-fuels to meet the global energy requirements by human being has intensified the concerns of increasing concentrations of greenhouse gases. Therefore, serious efforts are required to develop nonfossil-based renewable energy sources. Plants are more efficient in utilizing solar energy to convert it into biomass which can be used as feedstocks for biofuel production. Hence with the increasing demands of energy and the needs of cost-effective, sustainable production of fuels, it has become necessary to switch over to plant biomass as a renewable source of energy. Biofuels derived from more sustainable biological materials such as lignocellulosic plant residues, considered as second generation biofuels, are more dependable. However, there are technical challenges such as pretreatment and hydrolysis of lignocellulosic biomass to convert it into fermentable sugars. Plant genetic engineering has already proven its potential in modifying cell wall composition of plants for enhancing the efficiency of biofuel production. Interest and potential in the area are very much evident from the growing number of patents in the recent years on the subject. In this review, recent trends in genetic engineering of energy crops for biofuel production have been introduced, and strategies for the future developments have been discussed.
Multiple sequence alignment (MSA) is one of the topics of bio informatics that has seriously been researched. It is known as NP-complete problem. It is also considered as one of the most important and daunting tasks in computational biology. Concerning this a wide number of heuristic algorithms have been proposed to find optimal alignment. Among these heuristic algorithms are genetic algorithms (GA). The GA has mainly two major weaknesses: it is time consuming and can cause local minima. One of the significant aspects in the GA process in MSA is to maximize the similarities between sequences by adding and shuffling the gaps of Solution Coding (SC). Several ways for SC have been introduced. One of them is the Permutation Coding (PC). We propose a hybrid algorithm based on genetic algorithms (GAs) with a PC and 2-opt algorithm. The PC helps to code the MSA solution which maximizes the gain of resources, reliability and diversity of GA. The use of the PC opens the area by applying all functions over permutations for MSA. Thus, we suggest an algorithm to calculate the scoring function for multiple alignments based on PC, which is used as fitness function. The time complexity of the GA is reduced by using this algorithm. Our GA is implemented with different selections strategies and different crossovers. The probability of crossover and mutation is set as one strategy. Relevant patents have been probed in the topic.
The present world energy situation urgently requires exploring and developing alternate, sustainable sources for fuel. Biofuels have proven to be an effective energy source but more needs to be produced to meet energy goals. Whereas first generation biofuels derived from mainly corn and sugarcane continue to be used and produced, the contentious debate between "feedstock versus foodstock" continues. The need for sources that can be grown under different environmental conditions has led to exploring newer sources. Lignocellulosic biomass is an attractive source for production of biofuel, but pretreatment costs to remove lignin are high and the process is time consuming. Genetically modified plants that have increased sugar or starch content, modified lignin content, or produce cellulose degrading enzymes are some options that are being explored and tested. This review focuses on current research on increasing production of biofuels by genetic engineering of plants to have desirable characteristics. Recent patents that have been filed in this area are also discussed.
A technique has emerged over the past decade combining chromatin immunoprecipitation with DNA microarray analysis. This is a powerful and sensitive strategy that has been used extensively to characterise protein interactions with chromatin and epigenetic changes such as acetylation and methylation throughout the genome of different organisms. This technique has revolutionised our understanding of molecular genomics, continues to be widely used and is currently being applied in novel areas of cancer research. In this publication we review the historical context of this technology and offer current and future perspectives on how this technique is currently being developed and modified to allow its use in novel areas of research. We discuss the potential for this technique and its ongoing important role in biological research particularly in relation to cancer research. We also offer insight into the potential clinical application of this technology in stratified medicine, particularly in the field of cancer therapy.
Endometriosis is a gynecological disease that affects up to 10%-15% of all reproductive-age women worldwide. It is characterized by the presence of endometrial tissues outside the uterine cavity. Endometriosis is a complex disease; its pathogenesis includes altered steroid metabolism and immune system abnormalities such as inflammation, increased angiogenic activity in the peritoneal fluid and impaired recognition of ectopic endometrial cells. The development of endometriosis also depends on genetic, anatomical and environmental factors. Numerous surgical and medical approaches to treat endometriosis have been developed to date. However, complete resolution of the problem has not been achieved so far. Gene therapy holds exciting promise for the treatment of numerous disorders and current studies have indicated it can also be applied to endometriosis. The focus of this review is to summarize the pathogenetic background of the disease and to highlight current gene therapy approaches for this common gynecological disorder.
The grain amaranths were important food crops for the ancient middle and South American civilization. The germplasm of amaranths also has not been well characterized from the point of view of its exploitation for improvement of amaranths in general, a grain amaranth in particular. Among all under exploited crops grain amaranth is the most suitable candidate to begin with. As it is one of the most important under exploited crops being used as subsidiary or supplementary food. This work will report a study concerning the patent related to the biotechnological applications of Amaranths. It has been summarized in results that RAPD is a powerful approach to understand both inter-as-well as intra species relationships in the genus amaranths. One result indicates the presence of at least two repetitive families, such that at least one family of sequences is present in both cot1 as well as total nuclear DNA. The grain amaranth cultivation plays an important role in changing the economy of rural life. It is a source of dietary protein in strictly vegetarian people. In amaranths, somatic hybridization can be combined to the tertiary gene pools. Some of amaranth triploids are reported to be good in (Sharma SK, Dawson IK and Waugh R 1995) foliage and nutritional quality. They have broader leaves and good growth. Amaranth is grown under variety of soils and environmental conditions such as alkalinity, salinity, drought, frost etc. One of the ways to improve quality of grain amaranths to isolate variants of lysine genes products of which are enriched in essential amino acids. The high lysine content gene named as 'amargene' has been isolated and the patents have been used as biotechnological approach to introduce the gene in the tuber crop improvement The scope of biotechnology for the genetic improvement of grain amaranth crop has been described.
The Serine Protease Inhibitors (Serpins) have been a focus of research by biomedical industries due to their critical role in human health. The use of serpin in the treatment of many diseases was widely investigated through the identification of new genes encoding these proteins in all kingdoms of life. The characterization of these genes revealed that they encoded proteins having low sequence homologies. Future developments are focusing not only on the protease inhibition activity, but also on the other effects due to the interactions of serpins with other components such as hormone transport. Here we give a concise overview of the most recent patents that have been reported in this field of research.
Protein kinase C (PKC) comprises a family of 10 serine/threonine kinases divided into 3 subfamilies: classical, novel and atypical. These isoenzymes represent one of the major mediators of signal transduction, and most may be associated with several pathogenic processes including malignant transformation or cancer and metastasis. Moreover, some activated isoenzymes are also involved in other diseases such as infarct, rejection due to incomplete histocompatibility in organ transplantation, pain, diabetic macular edema, etc. Here, we review several patents related to inhibitors of PKC that represent a new and promising strategy for the prevention and treatment of these illnesses. Among these inhibitors, we included antisense oligonucleotides as another useful strategy to treat infectious and autoimmune diseases associated with misregulated expression of PKC and tumour necrosis factor alpha (TNF-α). On the other hand, two different activators of PKC and their applications related to neurodegenerative diseases have also been reviewed in this work.
In this paper we present a method for finding infrequent simple motifs in a finite set of sequences. The method uses a lattice structure and minimal forbidden patterns. It is based on a method for solving the Simple Motif Problem and has the potential to discover new patents in biological macromolecules. Indeed, the extracted motifs can help biologists to learn about the biological functions of these macromolecules and, consequently, can help them to understand the mechanisms of the biological processes in which these sequences are involved.
In this paper, we present efficient algorithms for finding indeterminate Arc-Annotated patterns in indeterminate Arc-Annotated references. Our algorithms run in O(m+ (nm) w) time where n and m are respectively the length of our reference and pattern strings and w is the target machine word size. Here we have assumed the alphabet size to be constant, because, indeterminate Arc-Annotated sequences are used to model biological sequences. Clearly, for short patterns, our algorithms run in linear time and efficient algorithms for matching short patterns to reference genomes have huge applications in practical settings. We have also applied our algorithms to scan the ncRNAs without pseudoknots. We scanned three whole human chromosomes and it took only 2.5 - 4 minutes to scan one whole chromosome for an ncRNA family. Some relevant patents are discussed in.
Motif finding in DNA, RNA and proteins plays an important role in life science research. Recent patents concerning motif finding in biomolecular data are recorded in the DNA Patent Database which serves as a resource for policy makers and members of the general public interested in fields like genomics, genetics and biotechnology. In this paper, we present a computational approach to mining for RNA tertiary motifs in genomic sequences. Specifically, we describe a method, named CSminer, and show, as a case study, the application of CSminer to genome-wide search for coaxial helical stackings in RNA 3-way junctions. A coaxial helical stacking occurs in an RNA 3-way junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Experimental results demonstrate the effectiveness of our approach.
MOTIVATION Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality part of the read allowing a number of mismatches and the insertion of a single gap in the alignment. RESULTS We present GapMis, a tool for pairwise sequence alignment with a single gap. It is based on a simple algorithm, which computes a different version of the traditional dynamic programming matrix. The presented experimental results demonstrate that GapMis is more suitable and efficient than most popular tools for this task.
An absent word (also called a forbidden word or an unword in other contexts) in a sequence is a segment that does not appear in the given sequence. It is a minimal absent word if all its proper factors occur in the given sequence. In this article, we review the concept of minimal absent words, which includes the notion of shortest absent words but is much stronger. We present an efficient method for computing the minimal absent words of bounded length for DNA sequence using a Trie of bounded depth, representing bounded length factors. This method outputs the whole set of minimal absent words and furthermore our technique provides a linear-time algorithm with less memory usage than previous solutions. We also present an approach to distinguish sequences of different organisms using their minimal absent words. Our solution applies a length-weighted index to discriminate sequences and the results show that we can build phylogenetic tree based on the patent collected information.
Most types of bacteria produce bacteriocins, which are proteinaceous extracellular compounds that can inhibit the growth of other undesirable microorganisms. Bacteriocins are receiving increasing attention, due to their many applications, ranging from their initial application in strategies for food preservation to more recent proposed uses in biomedical strategies aimed at fighting certain bacterial infections. Thus, while nisin has a long history of use as a safe additive in certain food products for the purpose of food preservation, certain bacteriocin-producing lactic acid bacteria, which are generally recognised as safe microorganisms, or their extracellular extracts are receiving increased attention as protective cultures or antimicrobial extracts in minimally processed food products. More recently, a number of these bacteriocinproducing cultures have been proposed for use in other applications, such as in probiotics, for the inhibition of biofilms in the food industry, or even as coadjuvants of combined therapeutical strategies along with other antimicrobial agents in biomedical applications. This review aims to provide a brief overview of the most relevant recent patents in this field.
