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1.	Dennison, M. J., et al. (författare) Biosensors for environmental monitoring 1995 Ingår i: Biotechnology Advances. - : Elsevier. - 0734-9750 .- 1873-1899. ; 13:1, s. 1-12 Forskningsöversikt (refereegranskat)abstract Increasing environmental legislation which controls the release and the levels of certain chemicals in the environment has created a need for reliable monitoring of these substances in air, soil and especially water. Conventional analytical techniques, although highly precise, suffer from the disadvantages of high cost, the need for trained personnel and the fact that they are mostly laboratory bound. Biosensors because of their specificity, fast response times, low cost, portability, ease of use and a continuous real time signal, can present distinct advantages in certain cases. Their biological base makes them ideal for toxicological measurements which are suited for health and safety applications. Over the last 3–4 years there has been an increase in the number of publications concerning biosensors for environmental monitoring, especially in the field of pesticide measurements.
2.	Shionoya, Kiseko, 1964-, et al. (författare) Immobilized enzyme film, protein immobilized film and process for forming the same : Patent abstracts. Patent No. 5356757 1995 Ingår i: Biotechnology Advances. - : Elsevier. - 0734-9750 .- 1873-1899. ; 13:2, s. 300-300 Tidskriftsartikel (refereegranskat)abstract Disclosed are an immobilized enzyme film, characterized in that said film is formed using an enzyme solution prepared by adding 1 to 3 parts by weight of a 50 to 100 wt % water-soluble crosslinking agent having at least two epoxy groups in the molecule and 1 to 3 parts by weight of a 1 to 2 wt % glutaraldehyde to 1 to 3 parts by weight of a 10 to 50 wt % aqueous protein solution containing an enzyme, and a process for forming the same on an ion-sensitive field effect transistor. The thus formed immobilized enzyme film is of an uniform thickness and stable by virtue of its increased hydrophilicity and higher elasticity, whereby deactivation of the enzyme to be caused by the shrinkage of the film can be prevented.
3.	Abdelaziz, Omar Y., et al. (författare) Biological valorization of low molecular weight lignin 2016 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 34:8, s. 1318-1346 Forskningsöversikt (refereegranskat)abstract Lignin is a major component of lignocellulosic biomass and as such, it is processed in enormous amounts in the pulp and paper industry worldwide. In such industry it mainly serves the purpose of a fuel to provide process steam and electricity, and to a minor extent to provide low grade heat for external purposes. Also from other biorefinery concepts, including 2nd generation ethanol, increasing amounts of lignin will be generated. Other uses for lignin – apart from fuel production – are of increasing interest not least in these new biorefinery concepts. These new uses can broadly be divided into application of the polymer as such, native or modified, or the use of lignin as a feedstock for the production of chemicals. The present review focuses on the latter and in particular the advances in the biological routes for chemicals production from lignin. Such a biological route will likely involve an initial depolymerization, which is followed by biological conversion of the obtained smaller lignin fragments. The conversion can be either a short catalytic conversion into desired chemicals, or a longer metabolic conversion. In this review, we give a brief summary of sources of lignin, methods of depolymerization, biological pathways for conversion of the lignin monomers and the analytical tools necessary for characterizing and evaluating key lignin attributes.
4.	Aminian-Dehkordi, Javad, et al. (författare) Synthetic biology tools for environmental protection 2023 Ingår i: Biotechnology Advances. - 0734-9750. ; 68 Forskningsöversikt (refereegranskat)abstract Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.
5.	Ansell, Brendan R. E., et al. (författare) Drug resistance in Giardia duodenalis 2015 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 33:6, s. 888-901 Forskningsöversikt (refereegranskat)abstract Giardia duodenalis is a microaerophilic parasite of the human gastrointestinal tract and a major contributor to diarrheal and post-infectious chronic gastrointestinal disease world-wide. Treatment of G. duodenalis infection currently relies on a small number of drug classes. Nitroheterocyclics, in particular metronidazole, have represented the front line treatment for the last 40 years. Nitroheterocyclic-resistant G. duodenalis have been isolated from patients and created in vitro, prompting considerable research into the biomolecular mechanisms of resistance. These compounds are redox-active and are believed to damage proteins and DNA after being activated by oxidoreductase enzymes in metabolically active cells. In this review, we explore the molecular phenotypes of nitroheterocyclic-resistant G. duodenalis described to date in the context of the protisfs unusual glycolytic and antioxidant systems. We propose that resistance mechanisms are likely to extend well beyond currently described resistance-associated enzymes (i.e., pyruvate ferredoxin oxidoreductases and nitroreductases), to include NAD(P)H- and flavin-generating pathways, and possibly redox-sensitive epigenetic regulation. Mechanisms that allow G. duodenalis to tolerate oxidative stress may lead to resistance against both oxygen and nitroheterocyclics, with implications for clinical control. The present review highlights the potential for systems biology tools and advanced bioinformatics to further investigate the multifaceted mechanisms of nitroheterocyclic resistance in this important pathogen.
6.	Cámara, Elena, 1985, et al. (författare) Data mining of Saccharomyces cerevisiae mutants engineered for increased tolerance towards inhibitors in lignocellulosic hydrolysates 2022 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 57 Forskningsöversikt (refereegranskat)abstract The use of renewable plant biomass, lignocellulose, to produce biofuels and biochemicals using microbial cell factories plays a fundamental role in the future bioeconomy. The development of cell factories capable of efficiently fermenting complex biomass streams will improve the cost-effectiveness of microbial conversion processes. At present, inhibitory compounds found in hydrolysates of lignocellulosic biomass substantially influence the performance of a cell factory and the economic feasibility of lignocellulosic biofuels and chemicals. Here, we present and statistically analyze data on Saccharomyces cerevisiae mutants engineered for altered tolerance towards the most common inhibitors found in lignocellulosic hydrolysates: acetic acid, formic acid, furans, and phenolic compounds. We collected data from 7971 experiments including single overexpression or deletion of 3955 unique genes. The mutants included in the analysis had been shown to display increased or decreased tolerance to individual inhibitors or combinations of inhibitors found in lignocellulosic hydrolysates. Moreover, the data included mutants grown on synthetic hydrolysates, in which inhibitors were added at concentrations that mimicked those of lignocellulosic hydrolysates. Genetic engineering aimed at improving inhibitor or hydrolysate tolerance was shown to alter the specific growth rate or length of the lag phase, cell viability, and vitality, block fermentation, and decrease product yield. Different aspects of strain engineering aimed at improving hydrolysate tolerance, such as choice of strain and experimental set-up are discussed and put in relation to their biological relevance. While successful genetic engineering is often strain and condition dependent, we highlight the conserved role of regulators, transporters, and detoxifying enzymes in inhibitor tolerance. The compiled meta-analysis can guide future engineering attempts and aid the development of more efficient cell factories for the conversion of lignocellulosic biomass.
7.	Dan, Meiling, et al. (författare) Current insights of factors interfering the stability of lytic polysaccharide monooxygenases 2023 Ingår i: Biotechnology Advances. - : Elsevier. - 0734-9750 .- 1873-1899. ; 67, s. 108216-108216 Tidskriftsartikel (refereegranskat)abstract Cellulose and chitin are two of the most abundant biopolymers in nature, but they cannot be effectively utilized in industry due to their recalcitrance. This limitation was overcome by the advent of lytic polysaccharide monooxygenases (LPMOs), which promote the disruption of biopolymers through oxidative mechanism and provide a breakthrough in the action of hydrolytic enzymes. In the application of LPMOs to biomass degradation, the key to consistent and effective functioning lies in their stability. The efficient transformation of biomass resources using LPMOs depends on factors that interfere with their stability. This review discussed three aspects that affect LPMO stability: general external factors, structural factors, and factors in the enzyme-substrate reaction. It explains how these factors impact LPMO stability, discusses the resulting effects, and finally presents relevant measures and considerations, including potential resolutions. The review also provides suggestions for the application of LPMOs in polysaccharide degradation.
8.	Golovitchev, Valeri, 1945, et al. (författare) Construction of combusiton models for rapeseed methyl ester bio-diesel fuel for internal combusiton engine aplications 2009 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 27:5, s. 641-655 Tidskriftsartikel (refereegranskat)abstract Bio-diesel fuels refer to non-petroleum based diesel fuels consisting of long chain alkyl esters produced by transesterifcation of vegetable oils, and proposed to be used (as neat or blended with conventional fuels) in unmodified diesel engines. Currently, there are few papers (see e.g. [1,2]) in which theoretical models for bio-diesel (e.g. RME) combustion simulations were reported. The models, developed in this paper, are modifications of those described in [1]. After the compilation of liquid fuel properties, the existing detailed mechanism of methyl butanoate ester, C5H10O2 [2, 3] oxidation was supplemented by sub-mechanisms for two proposed fuel constituent components, C7H16 and C7H8O (and, then, by mp2d and propyne, C3H4) to represent the combustion model of RME described by the chemical formula, C19H34O2 (or C19H36O2). The main fuel vapor thermal properties were taken as those of methyl palmitate C19H36O2 in the NASA polynomial form of the Burcat [4] database. The special global reaction was introduced to “crack” the main fuel into constituent components, which sub-mechanisms were collected in the general (309 species, 1472 reactions) including also soot and NOx formation processes. The detailed combustion mechanism was validated using shock-tube ignition-delay data at diesel engine conditions. For constant volume and diesel engine (Volvo D12C) combustion modeling, this mechanism was reduced to 88 species participating in 363 reactions.
9.	Jullesson, David, 1987, et al. (författare) Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals 2015 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 33:7, s. 1395-1402 Forskningsöversikt (refereegranskat)abstract Industrial bio-processes for fine chemical production are increasingly relying on cell factories developed through metabolic engineering and synthetic biology. The use of high throughput techniques and automation for the design of cell factories, and especially platform strains, has played an important role in the transition from laboratory research to industrial production. Model organisms such as Saccharomyces cerevisiae and Escherichia coli remain widely used host strains for industrial production due to their robust and desirable traits. This review describes some of the bio-based fine chemicals that have reached the market, key metabolic engineering tools that have allowed this to happen and some of the companies that are currently utilizing these technologies for developing industrial production processes.
10.	Kumar, Saroj, et al. (författare) Covalent and non-covalent chemical engineering of actin for biotechnological applications 2017 Ingår i: Biotechnology Advances. - : Elsevier. - 0734-9750 .- 1873-1899. ; 35:7, s. 867-888 Forskningsöversikt (refereegranskat)abstract The cytoskeletal filaments are self-assembled protein polymers with 8-25 nm diameters and up to several tens of micrometres length. They have a range of pivotal roles in eukaryotic cells, including transportation of intracellular cargoes (primarily microtubules with dynein and kinesin motors) and cell motility (primarily actin and myosin) where muscle contraction is one example. For two decades, the cytoskeletal filaments and their associated motor systems have been explored for nanotechnological applications including miniaturized sensor systems andlab-on-a-chip devices. Several developments have also revolved around possible exploitation of the filaments alone without their motor partners. Efforts to use the cytoskeletal filaments for applications often require chemical or genetic engineering of the filaments such as specific conjugation with fluorophores, antibodies, oligonucleotides or various macromolecular complexes e.g. nanoparticles. Similar conjugation methods are also instrumental for a range of fundamental biophysical studies. Here we review methods for non-covalent and covalent chemical modifications of actin filaments with focus on critical advantages and challenges of different methods as well as critical steps in the conjugation procedures. We also review potential uses of the engineered actin filaments in nanotechnological applications and in some key fundamental studies of actin and myosin function. Finally, we consider possible future lines of investigation that may be addressed by applying chemical conjugation of actin in new ways.
11.	Mahboubi, Amir, et al. (författare) Reverse membrane bioreactor : Introduction to a new technology for biofuel production 2016 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 34:5, s. 954-75 Tidskriftsartikel (refereegranskat)abstract The novel concept of reverse membrane bioreactors (rMBR) introduced in this review is a new membrane-assisted cell retention technique benefiting from the advantageous properties of both conventional MBRs and cell encapsulation techniques to tackle issues in bioconversion and fermentation of complex feeds. The rMBR applies high local cell density and membrane separation of cell/feed to the conventional immersed membrane bioreactor (iMBR) set up. Moreover, this new membrane configuration functions on basis of concentration-driven diffusion rather than pressure-driven convection previously used in conventional MBRs. These new features bring along the exceptional ability of rMBRs in aiding complex bioconversion and fermentation feeds containing high concentrations of inhibitory compounds, a variety of sugar sources and high suspended solid content. In the current review, the similarities and differences between the rMBR and conventional MBRs and cell encapsulation regarding advantages, disadvantages, principles and applications for biofuel production are presented and compared. Moreover, the potential of rMBRs in bioconversion of specific complex substrates of interest such as lignocellulosic hydrolysate is thoroughly studied.[on SciFinder (R)]
12.	Mao, Jiwei, 1990, et al. (författare) Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms 2024 Ingår i: Biotechnology Advances. - 0734-9750. ; 74 Forskningsöversikt (refereegranskat)abstract Metabolic burden is defined by the influence of genetic manipulation and environmental perturbations on the distribution of cellular resources. The rewiring of microbial metabolism for bio-based chemical production often leads to a metabolic burden, followed by adverse physiological effects, such as impaired cell growth and low product yields. Alleviating the burden imposed by undesirable metabolic changes has become an increasingly attractive approach for constructing robust microbial cell factories. In this review, we provide a brief overview of metabolic burden engineering, focusing specifically on recent developments and strategies for diminishing the burden while improving robustness and yield. A variety of examples are presented to showcase the promise of metabolic burden engineering in facilitating the design and construction of robust microbial cell factories. Finally, challenges and limitations encountered in metabolic burden engineering are discussed.
13.	Meghwanshi, Gautam Kumar, et al. (författare) Archaeal lipolytic enzymes : Current developments and further prospects 2022 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 61 Forskningsöversikt (refereegranskat)abstract Lipolytic enzymes include triacylglycerol lipases (EC 3.1.1.3) and esterases (EC 3.1.1.1) that catalyze the cleavage and formation of ester bonds. They are potential industrial biocatalysts because of their broad range of activities on natural and synthetic substrates, high stability in organic solvents, thermal stability, stability in highly acidic and alkaline pH conditions and enantio-, regio-and chemo-selectivity. They also have varied ap-plications in different sectors, among which industrial biotechnology, the production of cleaning agents, and pharmaceuticals are the most important ones. Identifying extremophilic lipolytic enzymes is of paramount in-terest and is a growing field in academic and industrial research. This review is focused on the current knowledge and future avenues of investigation on lipolytic enzymes sourced from the underexploited archaeal domain. Archaea is a potential source for novel extremophilic enzymes, which have high demand in the industries. The archaeal lipases and esterases are clustered into different families based on their similarity/dissimilarity at the genetic level and protein structures. The updated information on characterized and putative lipase sequences has also been presented in this paper. Common structural scaffolds of archaeal lipases have been deduced and dis-cussed in this review. However, huge diversity at the level of their genetic sequences has yet to be correlated with the structure-function relationship. Based on their biochemical properties, possible applications and future prospective of archaeal lipolytic enzymes have also been proposed.
14.	Meng, Lingyin, 1991-, et al. (författare) Soft and flexible material-based affinity sensors 2020 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 39 Forskningsöversikt (refereegranskat)abstract Recent advances in biosensors and point-of-care (PoC) devices are poised to change and expand the delivery of diagnostics from conventional lateral-flow assays and test strips that dominate the market currently, to newly emerging wearable and implantable devices that can provide continuous monitoring. Soft and flexible materials are playing a key role in propelling these trends towards real-time and remote health monitoring. Affinity biosensors have the capability to provide for diagnosis and monitoring of cancerous, cardiovascular, infectious and genetic diseases by the detection of biomarkers using affinity interactions. This review tracks the evolution of affinity sensors from conventional lateral-flow test strips to wearable/implantable devices enabled by soft and flexible materials. Initially, we highlight conventional affinity sensors exploiting membrane and paper materials which have been so successfully applied in point-of-care tests, such as lateral-flow immunoassay strips and emerging microfluidic paper-based devices. We then turn our attention to the multifarious polymer designs that provide both the base materials for sensor designs, such as PDMS, and more advanced functionalised materials that are capable of both recognition and transduction, such as conducting and molecularly imprinted polymers. The subsequent content discusses wearable soft and flexible material-based affinity sensors, classified as flexible and skin-mountable, textile materials-based and contact lens-based affinity sensors. In the final sections, we explore the possibilities for implantable/injectable soft and flexible material-based affinity sensors, including hydrogels, microencapsulated sensors and optical fibers. This area is truly a work in progress and we trust that this review will help pull together the many technological streams that are contributing to the field.
15.	Muratovska, Nina, et al. (författare) Towards engineered yeast as production platform for capsaicinoids 2022 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 59 Forskningsöversikt (refereegranskat)abstract Capsaicinoids are bioactive alkaloids produced by the chili pepper fruit and are known to be the most potent agonists of the human pain receptor TRPV1 (Transient Receptor Potential Cation Channel Subfamily V Member 1). They are currently produced by extraction from chili pepper fruit or by chemical synthesis. Transfer of the biosynthetic route to a microbial host could enable more efficient capsaicinoid production by fermentation and may also enable the use of synthetic biology to create a diversity of new compounds with potentially improved properties. This review summarises the current state of the art on the biosynthesis of capsaicinoid precursors in baker's yeast, Saccharomyces cerevisiae, and discusses bioengineering strategies for achieving total synthesis from sugar.
16.	Nagarajan, Neerajha, et al. (författare) Enabling personalized implant and controllable biosystem development through 3D printing 2018 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 36:2, s. 521-533 Forskningsöversikt (refereegranskat)abstract The impact of additive manufacturing in our lives has been increasing constantly. One of the frontiers in this change is the medical devices. 3D printing technologies not only enable the personalization of implantable devices with respect to patient-specific anatomy, pathology and biomechanical properties but they also provide new opportunities in related areas such as surgical education, minimally invasive diagnosis, medical research and disease models. In this review, we cover the recent clinical applications of 3D printing with a particular focus on implantable devices. The current technical bottlenecks in 3D printing in view of the needs in clinical applications are explained and recent advances to overcome these challenges are presented. 3D printing with cells (bioprinting); an exciting subfield of 3D printing, is covered in the context of tissue engineering and regenerative medicine and current developments in bioinks are discussed. Also emerging applications of bioprinting beyond health, such as biorobotics and soft robotics, are introduced. As the technical challenges related to printing rate, precision and cost are steadily being solved, it can be envisioned that 3D printers will become common on-site instruments in medical practice with the possibility of custom-made, on-demand implants and, eventually, tissue engineered organs with active parts developed with biorobotics techniques.
17.	Ortiz Rios, Rodomiro Octavio (författare) From crossbreeding to biotechnology-facilitated improvement of banana and plantain 2014 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 32, s. 158–169- Tidskriftsartikel (refereegranskat)abstract The annual harvest of banana and plantain (Musa spp.) is approximately 145 million tons worldwide. About 85% of this global production comes from small plots and kitchen or backyard gardens from the developingworld, and only 15% goes to the export trade. Musa acuminata and Musa balbisiana are the ancestors of several hundreds of parthenocarpic Musa diploid and polyploid cultivars, which show multiple origins through inter- and intra-specific hybridizations from these two wild diploid species. Generating hybrids combining host plant resistance to pathogens and pests, short growth cycles and height, high fruit yield, parthenocarpy, and desired quality from the cultivars remains a challenge for Musa crossbreeding, which started about one century ago in Trinidad. The success of Musa crossbreeding depends on the production of true hybrid seeds in a crop known for its high levels of female sterility, particularly among polyploid cultivars. All banana export cultivars grown today are, however, selections from somatic mutants of the group Cavendish and have a very narrow genetic base, while smallholders in sub- Saharan Africa, tropical Asia and Latin America use some bred-hybrids (mostly cooking types). Musa improvement goals need to shift to address emerging threats because of the changing climate. Innovative cell and molecular biology tools have the potential to enhance the pace and efficiency of genetic improvement in Musa. Micropropagation has been successful for high throughput of clean plantingmaterials while in vitro seed germination assists in obtaining seedlings after inter-specific and across ploidy hybridization. Flow cytometry protocols are used for checking ploidy among genebank accessions and breeding materials. DNA markers, the genetic maps based on them, and the recent sequencing of the banana genome offer means for gaining more insights in the genetics of the crops and to identifying genes that could lead to accelerating Musa betterment. Likewise, DNA fingerprinting has been useful to characterize Musa diversity. Genetic engineering provides a complementary tool to Musa breeders who can introduce today transgenes that may confer resistance to bacteria, fungi and nematodes, or enhance pro-vitamin A fruit content. In spite of recent advances, the genetic improvement of Musa depends on a few crossbreeding programs (based in Brazil, Cameroon, Côte d'Ivoire, Guadeloupe, Honduras, India, Nigeria, Tanzania and Uganda) or a handful of genetic engineering endeavors (Australia, Belgium, India, Kenya, Malaysia and Uganda). Development investors (namely international aid and philanthropy) should therefore increase their funding to genetically enhance this crop that ranks among the 10-top staple foods of the developing world.
18.	Ortiz Rios, Rodomiro Octavio (författare) Haploids: Constraints and opportunities in plant breeding 2015 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 33, s. 812-829 Forskningsöversikt (refereegranskat)abstract The discovery of haploids in higher plants led to the use of doubled haploid (DH) technology in plant breeding. This article provides the state of the art on DH technology including the induction and identification of haploids, what factors influence haploid induction, molecular basis of microspore embryogenesis, the genetics underpinnings of haploid induction and its use in plant breeding, particularly to fix traits and unlock genetic variation. Both in vitro and in vivo methods have been used to induce haploids that are thereafter chromosome doubled to produce DH. Various heritable factors contribute to the successful induction of haploids, whose genetics is that of a quantitative trait. Genomic regions associated with in vitro and in vivo DH production were noted in various crops with the aid of DNA markers. It seems that F2 plants are the most suitable for the induction of DH lines than F1 plants. Identifying putative haploids is a key issue in haploid breeding. DH technology in Brassicas and cereals, such as barley, maize, rice, rye andwheat, has been improved and used routinely in cultivar development, while in other food staples such as pulses and root crops the technology has not reached to the stage leading to its application in plant breeding. The centromere-mediated haploid induction system has been used in Arabidopsis, but not yet in crops. Most food staples are derived from genomic resources-rich crops, including those with sequenced reference genomes. The integration of genomic resourceswith DH technology provides new opportunities for the improving selection methods, maximizing selection gains and accelerate cultivar development. Marker-aided breeding and DH technology have been used to improve host plant resistance in barley, rice, and wheat. Multinational seed companies are using DH technology in large-scale production of inbred lines for further development of hybrid cultivars, particularly in maize. The public sector provides support to national programs or small-medium private seed for the exploitation of DH technology in plant breeding.
19.	Rahimi, Shadi, 1982, et al. (författare) Technologies for biological removal and recovery of nitrogen from wastewater 2020 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 43 Forskningsöversikt (refereegranskat)abstract Water contamination is a growing environmental issue. Several harmful effects on human health and the environment are attributed to nitrogen contamination of water sources. Consequently, many countries have strict regulations on nitrogen compound concentrations in wastewater effluents. Wastewater treatment is carried out using energy- and cost-intensive biological processes, which convert nitrogen compounds into innocuous dinitrogen gas. On the other hand, nitrogen is also an essential nutrient. Artificial fertilizers are produced by fixing dinitrogen gas from the atmosphere, in an energy-intensive chemical process. Ideally, we should be able to spend less energy and chemicals to remove nitrogen from wastewater and instead recover a fraction of it for use in fertilizers and similar applications. In this review, we present an overview of various technologies of biological nitrogen removal including nitrification, denitrification, anaerobic ammonium oxidation (anammox), as well as bioelectrochemical systems and microalgal growth for nitrogen recovery. We highlighted the nitrogen removal efficiency of these systems at different temperatures and operating conditions. The advantages, practical challenges, and potential for nitrogen recovery of different treatment methods are discussed.
20.	Rahimi, Shadi, 1982, et al. (författare) Triterpenoid-biosynthetic UDP-glycosyltransferases from plants 2019 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 37:7 Forskningsöversikt (refereegranskat)abstract Triterpenoid saponins are naturally occurring structurally diverse glycosides of triterpenes that are widely distributed among plant species. Great interest has been expressed by pharmaceutical and agriculture industries for the glycosylation of triterpenes. Such modifications alter their taste and bio-absorbability, affect their intra−/extracellular transport and storage in plants, and induce novel biological activities in the human body. Uridine diphosphate (UDP)-glycosyltransferases (UGTs) catalyze glycosylation using UDP sugar donors. These enzymes belong to a multigene family and recognize diverse natural products, including triterpenes, as the acceptor molecules. For this review, we collected and analyzed all of the UGT sequences found in Arabidopsis thaliana as well as 31 other species of triterpene-producing plants. To identify potential UGTs with novel functions in triterpene glycosylation, we screened and classified those candidates based on similarity with UGTs from Panax ginseng, Glycine max, Medicago truncatula, Saponaria vaccaria, and Barbarea vulgaris that are known to function in glycosylate triterpenes. We highlight recent findings on UGT inducibility by methyl jasmonate, tissue-specific expression, and subcellular localization, while also describing their catalytic activity in terms of regioselectivity for potential key UGTs dedicated to triterpene glycosylation in plants. Discovering these new UGTs expands our capacity to manipulate the biological and physicochemical properties of such valuable molecules.
21.	Rosinha Grundtvig, Inês P., et al. (författare) Screening of organic solvents for bioprocesses using aqueous-organic two-phase systems 2018 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 36:7, s. 1801-1814 Tidskriftsartikel (refereegranskat)abstract The application of conventional organic solvents has been essential in several steps of bioprocesses in order to achieve sufficient economic efficiency. The use of organic solvents is frequently used either to partly or fully replace water in the reaction medium or as a process aid for downstream separation. Nowadays, manufacturers are increasingly requested to avoid and substitute solvents with hazardous potential. Therefore, the solvent selection must account for potential environmental hazards, health and safety problems, in addition to fulfilling the ideal characteristics for application in a process. For the first time, criteria including Environment, Health and Safety (EHS), as well as the technical requirements for reaction and separation have been reviewed, collected and integrated in a single organic solvent screening strategy to be used as a guideline for narrowing down the list of solvents to test experimentally. Additionally, we have also included a solvent selection guide based on the methodology developed in the Innovative Medicines Initiative CHEM21 (IMI CHEM21) project and applied specifically to water-immiscible solvents commonly used in bioprocesses.
22.	Roychoudhury, Pradip, et al. (författare) Synthesis, regulation and production of urokinase using mammalian cell culture: A comprehensive review 2006 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 24:5, s. 514-528 Forskningsöversikt (refereegranskat)abstract Urokinase, a serine protease, catalyzes the conversion of plasminogen to plasmin, which is responsible for dissolution of clots in blood vessels. It is an important drug for treatment of thromboembolic disease. Production of urokinase by mammalian cell culture has the following important steps: synthesis, regulation and secretion. Production and accumulation of this product in a bioreactor is a real challenge for biochemical engineers. Considerable information at molecular level needs to be understood for production of urokinase in order to correlate different parameters, which in turn can maximize the productivity. This information will be highlighted in this review. Moreover, urokinase production is a product-inhibited process. Therefore, in situ urokinase separation strategy is required to operate a bioreactor at its maximum urokinase formation rate. Integrated urokinase production and isolation processes developed recently will also be discussed briefly in this review. (c) 2006 Elsevier Inc. All rights reserved.
23.	Sekretaryova, Alina, et al. (författare) Bioelectrocatalytic systems for health applications 2016 Ingår i: Biotechnology Advances. - : Elsevier. - 0734-9750 .- 1873-1899. ; 34:3, s. 177-197 Forskningsöversikt (refereegranskat)abstract We present a brief overview of bioelectrocatalytic devices for in vitro health applications, including food safety and environmental analysis, focusing on microelectrode- and microfluidic-based biosensors, paper-based point-of-care devices and wearable biosensors. The main hurdles and future perspectives are discussed. We then consider the role of electron transfer between a biocatalyst and an electrode in biosensor design. Brief descriptions of indirect, direct and mediated mechanisms are given. The principal strategies, as well as recent developments for modulation of electron transfer in biocatalytic systems are summarised. In conclusion, we highlight some of the challenges associated with improving these redox systems.
24.	Shakeri Yekta, Sepehr, et al. (författare) Sulfide in engineered methanogenic systems - Friend or foe? 2023 Ingår i: Biotechnology Advances. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0734-9750 .- 1873-1899. ; 69 Forskningsöversikt (refereegranskat)abstract Sulfide ions are regarded to be toxic to microorganisms in engineered methanogenic systems (EMS), where organic substances are anaerobically converted to products such as methane, hydrogen, alcohols, and carboxylic acids. A vast body of research has addressed solutions to mitigate process disturbances associated with high sulfide levels, yet the established paradigm has drawn the attention away from the multifaceted sulfide interactions with minerals, organics, microbial interfaces and their implications for performance of EMS. This brief review brings forward sulfide-derived pathways other than toxicity and with potential significance for anaerobic organic matter degradation. Available evidence on sulfide reactions with organic matter, interventions with key microbial metabolisms, and interspecies electron transfer are critically synthesized as a guidance for comprehending the sulfide effects on EMS apart from the microbial toxicity. The outcomes identify existing knowledge gaps and specify future research needs as a step forward towards realizing the potential of sulfide-derived mechanisms in diversifying and optimizing EMS applications.
25.	Skoog, Emma, 1983, et al. (författare) Biobased adipic acid – The challenge of developing the production host 2018 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 36:8, s. 2248-2263 Forskningsöversikt (refereegranskat)abstract Adipic acid is a platform chemical, and is the most important commercial dicarboxylic acid. It has been targeted for biochemical conversion as an alternative to present chemical production routes. From the perspective of bioeconomy, several kinds of raw material are of interest including the sugar platform (derived from starch, cellulose or hemicellulose), the lignin platform (aromatics) and the fatty acid platform (lipid derived). Two main biochemical-based production schemes may be employed: (i) direct fermentation to adipic acid, or (ii) fermentation to muconic or glucaric acid, followed by chemical hydrogenation (indirect fermentation). This review presents a comprehensive description of the metabolic pathways that could be constructed and analyzes their respective theoretical yields and metabolic constraints. The experimental yields and titers obtained so far are low, with the exception of processes based on palm oil and glycerol, which have been reported to yield up to 50 g and 68 g adipic acid/L, respectively. The challenges that remain to be addressed in order to achieve industrially relevant production levels include solving redox constraints, and identifying and/or engineering enzymes for parts of the metabolic pathways that have yet to be metabolically demonstrated. This review provides new insights into ways in which metabolic pathways can be constructed to achieve efficient adipic acid production. The production host provides the chassis to be engineered via an appropriate metabolic pathway, and should also have properties suitable for the industrial production of adipic acid. An acidic process pH is attractive to reduce the cost of downstream processing. The production host should exhibit high tolerance to complex raw material streams and high adipic acid concentrations at acidic pH.
26.	Steffen-Munsberg, Fabian, et al. (författare) Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications 2015 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 33:5, s. 566-604 Tidskriftsartikel (refereegranskat)abstract In this review we analyse structure/sequence-function relationships for the superfamily of PLP-dependent enzymes with special emphasis on class III transaminases. Amine transaminases are highly important for applications in biocatalysis in the synthesis of chiral amines. In addition, other enzyme activities such as racemases or decarboxylases are also discussed. The substrate scope and the ability to accept chemically different types of substrates are shown to be reflected in conserved patterns of amino acids around the active site. These findings are condensed in a sequence-function matrix, which facilitates annotation and identification of biocatalytically relevant enzymes and protein engineering thereof.
27.	Šuchová, Katarína, et al. (författare) Cellulose- and xylan-degrading yeasts: Enzymes, applications and biotechnological potential 2022 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 59 Forskningsöversikt (refereegranskat)abstract Microbes and their carbohydrate-active enzymes are central for depolymerization of complex lignocellulosic polysaccharides in the global carbon cycle. Their unique abilities to degrade and ferment carbohydrates are also utilized in many industrial processes such as baking, brewing and production of biofuels and drugs. Effective degradation and utilization of cellulose and hemicelluloses is important for the shift towards green bioeconomy, and requires microbes equipped with proper sets of carbohydrate-active enzymes (CAZymes). Knowledge of cellulolytic and xylanolytic CAZymes has mainly been generated from bacteria and filamentous fungi, while yeasts have been largely overlooked and may represent an untapped resource in natural CAZymes with industrial relevance. Cellulose and xylan-degrading yeasts with the ability to ferment saccharides are also promising candidates for consolidated bioprocesses (CBPs), as they can degrade lignocellulose and utilize its constituents to produce desired products at the same time. Cellulolytic yeasts able to utilize insoluble crystalline cellulose are rare while xylanolytic yeasts are rather widespread in nature. The lack of particular enzymes in yeasts can be remediated by introducing the missing enzymes into strains having outstanding product-forming attributes. In this review, we provide a comprehensive overview of the cellulose- and xylan-degrading ascomycetous and basidiomycetous yeasts known to date. We describe how these yeasts can be identified through bioprospecting and bioinformatic approaches and summarize available growth and enzymatic assays for strain characterization. Known and predicted CAZymes are extensively analyzed, both in individual species and in a phylogenetic perspective. We also describe the strategies used for construction of recombinant cellulolytic and xylanolytic strains as well as current applications for polysaccharide-degrading yeasts. Finally, we discuss the great potential of these yeasts as industrial cell factories, identify open research questions and provide suggestions for future investigations.
28.	Udatha, Gupta, 1984, et al. (författare) The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases 2011 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 29:1, s. 94-110 Tidskriftsartikel (refereegranskat)abstract One of the most intriguing groups of enzymes, the feruloyl esterases (FAEs), is ubiquitous in both simple and complex organisms. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing high-added value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production and partial characterization of FAEs from fungi, while much less is known about FAEs of bacterial or plant origin. Initial classification studies on FAEs were restricted on sequence similarity and substrate specificity on just four model substrates and considered only a handful of FAEs belonging to the fungal kingdom. This study centers on the descriptor-based classification and structural analysis of experimentally verified and putative FAEs; nevertheless, the framework presented here is applicable to every poorly characterized enzyme family. 365 FAE-related sequences of fungal, bacterial and plantae origin were collected and they were clustered using Self Organizing Maps followed by k-means clustering into distinct groups based on amino acid composition and physico-chemical composition descriptors derived from the respective amino acid sequence. A Support Vector Machine model was subsequently constructed for the classification of new FAEs into the pre-assigned clusters. The model successfully recognized 98.2% of the training sequences and all the sequences of the blind test. The underlying functionality of the 12 proposed FAE families was validated against a combination of prediction tools and published experimental data. Another important aspect of the present work involves the development of pharmacophore models for the new FAE families, for which sufficient information on known substrates existed. Knowing the pharmacophoric features of a small molecule that are essential for binding to the members of a certain family opens a window of opportunities for tailored applications of FAEs.
29.	Wang, Shurong, et al. (författare) Comparison of the pyrolysis behavior of lignins from different tree species 2009 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 27:5, s. 562-567 Tidskriftsartikel (refereegranskat)abstract Despite the increasing importance of biomass pyrolysis. little is known about the pyrolysis behavior of lignin-one of the main components of biomass-due to its structural complexity and the difficulty in its isolation. In the present study, we extracted lignins from Manchurian ash (Fraxinus mandschurica) and Mongolian Scots pine (Pinus sylvestris var. mongolica) using the Bjorkman procedure, which has little effect on the structure of lignin. Fourier transform infrared (FTIR) spectrometry was used to characterize the microstructure of the Bjorkman lignins, i.e., milled wood lignins (MWLs), from the different tree species. The pyrolysis characteristics of MWLs were investigated using a thermogravimetric analyzer, and the release of the main volatile and gaseous products of pyrolysis were detected by FTIR spectroscopy. During the pyrolysis process, MWLs underwent thermodegradation over a wide temperature range. Manchurian ash MWL showed a much higher thermal degradation rate than Mongolian Scots pine MWL in the temperature range from 290-430 degrees C. High residue yields were achieved at 37 wt.% for Mongolian Scots pine MWL and 26 wt.% for Manchurian ash MWL. In order to further investigate the mechanisms of lignin pyrolysis, we also analyzed the FTIR profiles for the main pyrolysis products (CO2, CO, methane, methanol, phenols and formaldehyde) and investigated the variation in pyrolysis products between the different MWLs.
30.	Wu, Di, et al. (författare) Biological and conventional food processing modifications on food proteins : Structure, functionality, and bioactivity 2020 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 40 Forskningsöversikt (refereegranskat)abstract Food proteins are important nutrients for human health and thus make significant contributions to the unique functions of different foods. The modification of proteins through physical and biological processing could improve the functional and nutritional properties of food products; these changes can be attributed to modifications in particle size, solubility, emulsion stability, secondary structure, as well as the bioactivities of the proteins. Physical processing treatments might promote physical phenomena, such as combined friction, collision, shear forces, turbulence, and cavitation of particles, and lead to changes in the particle sizes of proteins. The objective of this review is to illustrate the effect of physical and biological processing on the structure, and physical and chemical properties of food-derived proteins and provide insights into the mechanism underlying structural changes. Many studies have suggested that physical and biological processes, such as ultrasound treatment, high pressure homogenization, ball mill treatment, and enzymatic hydrolysis could affect the structure, physical properties, and chemical properties of food-derived proteins. Some important applications of food-derived proteins are also discussed based on the relationships between their physical, chemical, and functional properties. Perspectives from fundamental or practical research are also brought in to provide a complete picture of the currently available relevant data.
31.	Zhao, X. Q., et al. (författare) Metabolic engineering frontiers emerging with advanced tools and methodologies 2017 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 35:8, s. 933-933 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
32.	Zuo, Fanglei, et al. (författare) Engineer probiotic bifidobacteria for food and biomedical applications - Current status and future prospective 2020 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 45 Forskningsöversikt (refereegranskat)abstract Bifidobacteria are members of the human gut microbiota and have shown to exert beneficial effects on their host. Certain strains have a long history of safe and effective use as probiotics. Due to the lack of efficient genetic tools, however, little is known about the molecular mechanisms on which these health-promoting properties are based, thus limiting the synthetic biology applications in bifidobacteria. Here, we discuss the recent development of genetic tools and their engagement in engineering bifidobacteria for food and biomedical applications, from eliminating antibiotic resistance mobile elements and improving robustness to preventing pathogen infections and delivering therapeutics for cancer treatment. In addition, we highlight the application of emerging genome engineering techniques for manipulating the bifidobacterial genome. Finally, we provide our perspective on the future development of synthetic biology techniques and programmed probiotic bifidobacteria with enhanced robustness and designer functionalities.
33.	Österlund, Tobias, 1984, et al. (författare) Fifteen years of large scale metabolic modeling of yeast: Developments and impacts 2012 Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 30:5, s. 979-988 Forskningsöversikt (refereegranskat)abstract Since the first large-scale reconstruction of the Saccharomyces cerevisiae metabolic network 15 years ago the development of yeast metabolic models has progressed rapidly, resulting in no less than nine different yeast genome-scale metabolic models. Here we review the historical development of large-scale mathematical modeling of yeast metabolism and the growing scope and impact of applications of these models in four different areas: as guide for metabolic engineering and strain improvement, as a tool for biological interpretation and discovery, applications of novel computational framework and for evolutionary studies.

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