Sustainability of protein production by bioreactor processes using wind and solar power as energy sources

Food production account for significant share of global environmental impacts. Impacts are global warming, fresh water use, land use and some non-renewable substance consumption like phosphorous fertilizers. Because of non-sustainable food production, the world is heading to different crises. Both food- and freshwater crises and also land area and phosphorous fertilizer shortages are one of many challenges to overcome in near future. The major protein sources production amounts, their impacts on environment and uses are show in this thesis. In this thesis, a more sustainable than conventional way of biomass production for food use is introduced. These alternative production methods are photobioreactor process and syngas-based bioreactor process. The processes’ energy consumption and major inputs are viewed. Their environmental impacts are estimated. These estimations are the compared to conventional protein production’s impacts. The outcome of the research is that, the alternative methods can be more sustainable solutions for food production than conventional production. However, more research is needed to verify the exact impacts. Photobioreactor is more sustainable process than syngas-based bioreactor process, but it is more location depended and uses more land area than syngas-based process. In addition, the technology behind syngas-based application is still developing and it can be more efficient in the future.

Nitrogen Oxides Reduction Possibilities at Pulp Mill and Power Plant

Tutkimuksen tarkoituksena oli selvittää typenoksidien vähennysmahdollisuudet Stora Enson Varkauden tehtaiden sellutehtaalla ja voimalaitoksella. Tutkimuksessa käsiteltiin tehdasalueen suurimpia typenoksidien päästölähteitä: soodakattilaa, meesauunia, kuorikattilaa, öljykattilaa ja muovi-alumiinijakeen kaasutuslaitosta. Tutkimuksessa selvitettiin typenoksidipäästöjen syntymekanismit ja erilaisiin polttotekniikoihin soveltuvat typenoksidien vähennystekniikat. Varkauden tehtaiden typenoksidien vuosipäästö vuonna 2001 oli 836 tonnia. Kansallinen lainsäädäntö, kansainväliset sopimukset sekä paras käytettävissä oleva tekniikka (BAT) huomioiden selvitettiin kuhunkin kohteeseen parhaiten soveltuvat ratkaisut. Tutkimuksen perusteella laadittiin toimenpideohjelma, joka määrittelee suositeltavan toteutusjärjestyksen typenoksidien vähennystoimenpiteille. Toimenpideohjelman tärkeimpinä kriteereinä pidettiin vuonna 2004 tulevan uuden ympäristöluvan arvioituja luparajoja sekä toimenpiteiden kustannustehokkuutta. Toteutusjärjestyksessä ensimmäiseksi valittiin koeajojakson järjestäminen ajon optimoimiseksi kiertopetikattilalla ja toiseksi meesauunin ajon optimointi jatkuvatoimisen NOx-analysaattorin avulla. Seuraaviksi toimenpiteiksi ehdotettiin vertikaali-ilmajärjestelmän käyttöönottoa soodakattilalla sekä SNCR-järjestelmän asennusta kuorikattilalle. Saavutettava NOx-vähennys tulisi olemaan 10 – 45 % ja hinta 30 – 3573 EUR vähennettyä NOx-tonnia kohti. Tutkimuksen osana Ilmatieteen laitoksella teetetyn typenoksidien leviämisselvityksen mukaan Stora Enson tehtaiden NOx-päästöjen vaikutus Varkauden ilmanlaatuun on hyvin pieni. Suurin osa NOx-päästöistä aiheutuu liikenteestä.

Active sulphide mine tailings impoundments as sources of contaminated drainage: controlling factors, methods of characterisation and geochemical constraints for mitigation

Low quality mine drainage from tailings facilities persists as one of the most significant global environmental concerns related to sulphide mining. Due to the large variation in geological and environmental conditions at mine sites, universal approaches to the management of mine drainage are not always applicable. Instead, site-specific knowledge of the geochemical behaviour of waste materials is required for the design and closure of the facilities. In this thesis, tailings-derived water contamination and factors causing the pollution were investigated in two coeval active sulphide mine sites in Finland: the Hitura Ni mine and the Luikonlahti Cu-Zn-Co-Ni mine and talc processing plant. A hydrogeochemical study was performed to characterise the tailingsderived water pollution at Hitura. Geochemical changes in the Hitura tailings were evaluated with a detailed mineralogical and geochemical investigation (solid-phase speciation, acid mine drainage potential, pore water chemistry) and using a spatial assessment to identify the mechanisms of water contamination. A similar spatial investigation, applying selective extractions, was carried out in the Luikonlahti tailings area for comparative purposes (Hitura low-sulphide tailings vs. Luikonlahti sulphide-rich tailings). At both sites, hydrogeochemistry of tailings seepage waters was further characterised to examine the net results of the processes observed within the impoundments and to identify constraints for water treatment. At Luikonlahti, annual and seasonal variation in effluent quality was evaluated based on a four-year monitoring period. Observations pertinent to future assessment and mine drainage prevention from existing and future tailings facilities were presented based on the results. A combination of hydrogeochemical approaches provided a means to delineate the tailings-derived neutral mine drainage at Hitura. Tailings effluents with elevated Ni, SO₄ ^2- and Fe content had dispersed to the surrounding aquifer through a levelled-out esker and underneath the seepage collection ditches. In future mines, this could be avoided with additional basal liners in tailings impoundments where the permeability of the underlying Quaternary deposits is inadequate, and with sufficiently deep ditches. Based on the studies, extensive sulphide oxidation with subsequent metal release may already initiate during active tailings disposal. The intensity and onset of oxidation depended on e.g. the Fe sulphide content of the tailings, water saturation level, and time of exposure of fresh sulphide grains. Continuous disposal decreased sulphide weathering in the surface of low-sulphide tailings, but oxidation initiated if they were left uncovered after disposal ceased. In the sulphide-rich tailings, delayed burial of the unsaturated tailings had resulted in thick oxidized layers, despite the continuous operation. Sulphide weathering and contaminant release occurred also in the border zones. Based on the results, the prevention of sulphide oxidation should already be considered in the planning of tailings disposal, taking into account the border zones. Moreover, even lowsulphide tailings should be covered without delay after active disposal ceases. The quality of tailings effluents showed wide variation within a single impoundment and between the two different types of tailings facilities assessed. The affecting factors included source materials, the intensity of weathering of tailings and embankment materials along the seepage flow path, inputs from the process waters, the water retention time in tailings, and climatic seasonality. In addition, modifications to the tailings impoundment may markedly change the effluent quality. The wide variation in the tailings effluent quality poses challenges for treatment design. The final decision on water management requires quantification of the spatial and seasonal fluctuation at the site, taking into account changes resulting from the eventual closure of the impoundment. Overall, comprehensive hydrogeochemical mapping was deemed essential in the identification of critical contaminants and their sources at mine sites. Mineralogical analysis, selective extractions, and pore water analysis were a good combination of methods for studying the weathering of tailings and in evaluating metal mobility from the facilities. Selective extractions with visual observations and pH measurements of tailings solids were, nevertheless, adequate in describing the spatial distribution of sulphide oxidation in tailings impoundments. Seepage water chemistry provided additional data on geochemical processes in tailings and was necessary for defining constraints for water treatment.

Thylakoid Protein Phosphorylation in Regulation of Photosynthesis

Once the seed has germinated, the plant is forced to face all the environmental changes in its habitat. In order to survive, plants have evolved a number of different acclimation systems. The primary reaction behind plant growth and development is photosynthesis. Photosynthesis captures solar energy and converts it into chemical form. Photosynthesis in turn functions under the control of environmental cues, but is also affected by the growth, development, and metabolic state of a plant. The availability of solar energy fluctuates continuously, requiring non-stop adjustment of photosynthetic efficiency in order to maintain the balance between photosynthesis and the requirements and restrictions of plant metabolism. Tight regulation is required, not only to provide sufficient energy supply but also to prevent the damage caused by excess energy. The very first reaction of photosynthesis is splitting of water into the form of oxygen, hydrogen, and electrons. This most fundamental reaction of life is run by photosystem II (PSII), and the energy required for the reaction is collected by the light harvesting complex II (LHCII). Several proteins of the PSII-LHCII complex are reversibly phosphorylated according to the energy balance between photosynthesis and metabolism. Thylakoid protein phosphorylation has been under extensive investigation for over 30 years, yet the physiological role of phosphorylation remains elusive. Recently, the kinases behind the phosphorylation of PSII-LHCII proteins (STN7 and STN8) were identified and the knockout mutants of these kinases became available, providing powerful tools to elucidate the physiological role of PSII-LHCII phosphorylation. In my work I have used the stn7 and stn8 mutants in order to clarify the role of PSII-LHCII phosphorylation in regulation and protection of the photosynthetic machinery according to environmental cues. I show that STN7- dependent PSII-LHCII protein phosphorylation is required to balance the excitation energy distribution between PSII and PSI especially under low light intensities when the excitation energy transfer from LHC to PSII and PSI is efficient. This mechanism differs from traditional light quality-induced “state 1” – “state 2” transition and ensures fluent electron transfer from PSII to PSI under low light, yet having highest physiological relevance under fluctuating light intensity. STN8-dependent phosphorylation of PSII proteins, in turn, is required for fluent turn-over of photodamaged PSII complexes and has the highest importance upon prolonged exposure of the photosynthetic apparatus to excess light.

Regulation of photosynthetic electron transfer in plant chloroplasts

This thesis focuses on the molecular mechanisms regulating the photosynthetic electron transfer reactions upon changes in light intensity. To investigate these mechanisms, I used mutants of the model plant Arabidopsis thaliana impaired in various aspects of regulation of the photosynthetic light reactions. These included mutants of photosystem II (PSII) and light harvesting complex II (LHCII) phosphorylation (stn7 and stn8), mutants of energy-dependent non-photochemical quenching (NPQ) (npq1 and npq4) and of regulation of photosynthetic electron transfer (pgr5). All of these processes have been extensively investigated during the past decades, mainly on plants growing under steady-state conditions, and therefore many aspects of acclimation processes may have been neglected. In this study, plants were grown under fluctuating light, i.e. the alternation of low and high intensities of light, in order to maximally challenge the photosynthetic regulatory mechanisms. In pgr5 and stn7 mutants, the growth in fluctuating light condition mainly damaged PSI while PSII was rather unaffected. It is shown that the PGR5 protein regulates the linear electron transfer: it is essential for the induction of transthylakoid ΔpH that, in turn, activates energy-dependent NPQ and downregulates the activity of cytochrome b6f. This regulation was shown to be essential for the photoprotection of PSI under fluctuations in light intensity. The stn7 mutants were able to acclimate under constant growth light conditions by modulating the PSII/PSI ratio, while under fluctuating growth light they failed in implementing this acclimation strategy. LHCII phosphorylation ensures the balance of the excitation energy distribution between PSII and PSI by increasing the probability for excitons to be trapped by PSI. LHCII can be phosphorylated over all of the thylakoid membrane (grana cores as well as stroma lamellae) and when phosphorylated it constitutes a common antenna for PSII and PSI. Moreover, LHCII was shown to work as a functional bridge that allows the energy transfer between PSII units in grana cores and between PSII and PSI centers in grana margins. Consequently, PSI can function as a quencher of excitation energy. Eventually, the LHCII phosphorylation, NPQ and the photosynthetic control of linear electron transfer via cytochrome b6f work in concert to maintain the redox poise of the electron transfer chain. This is a prerequisite for successful plant growth upon changing natural light conditions, both in short- and long-term.

Indoor air quality at a waste incineration plant in Finland

Waste has been incinerated for energy utilization for more than a hundred years, but the harmful emissions emitted from the incineration plants did not begin to cause concern until the 1980s. Many plants were shutdown and the waste incineration plant in Kyläsaari Helsinki was one of them. In later years, new landfill regulations have increased the interest in waste incineration. During the last year, four new plants were taken into operation in Finland, Westenergy in Vaasa among them. The presence of dust has been observed indoors at Westenergy waste incineration plant. Dust is defined as particles with a diameter above 10 μm, while fine particles have a diameter smaller than 2.5 μm, ultrafine under 0.1 μm and nanoparticles under 0.05 μm. In recent years, the focus of particle health research has been changed to investigate smaller particles. Ultrafine particles have been found to be more detrimental to health than larger particles. Limit values regulating the concentrations of ultrafine particles have not been determined yet. The objective of this thesis was to investigate dust and particles present inside the Westenergy waste incineration facility. The task was to investigate the potential pollutant sources and to give recommendations of how to minimize the presence of dust and particles in the power plant. The total particle number concentrations and size distributions where measured at 15 points inside the plant with an Engine Exhaust Particle Sizer (EEPS) Spectrometer. The measured particles were mainly in the ultrafine size range. Dust was only visually investigated, since the main purpose was to follow the dust accumulation. The measurement points inside the incineration plant were chosen according to investigate exposure to visitors and workers. At some points probable leakage of emissions were investigated. The measurements were carried out during approximately one month in March–April 2013. The results of the measurements showed that elevated levels of dust and particles are present in the indoor air at the waste incineration plant. The cleanest air was found in the control room, warehouse and office. The most polluted air was near the sources that were investigated due to possible leakage and in the bottom ash hall. However, the concentrations were near measured background concentrations in European cities and no leakage could be detected. The high concentrations were assumed to be a result of a lot of dust and particles present on surfaces that had not been cleaned in a while. The main source of the dust and particles present inside the waste incineration plant was thought to be particles and dust from the outside air. Other activities in the area around the waste incineration facility are ground work activities, stone crushing and traffic, which probably are sources of particle formation. Filtration of the outside air prior entering the facility would probably save personnel and visitors from nuisance and save in cleaning and maintenance costs.

Functional Genomic Approaches for Deciphering Plant-Virus Interactions

Plant-virus interactions are very complex in nature and lead to disease and symptom formation by causing various physiological, metabolic and developmental changes in the host plants. These interactions are mainly the outcomes of viral hijacking of host components to complete their infection cycles and of host defensive responses to restrict the viral infections. Viral genomes contain only a small number of genes often encoding for multifunctional proteins, and all are essential in establishing a viral infection. Thus, it is important to understand the specific roles of individual viral genes and their contribution to the viral life cycles. Among the most important viral proteins are the suppressors of RNA silencing (VSRs). These proteins function to suppress host defenses mediated by RNA silencing and can also serve in other functions, e.g. in viral movement, transactivation of host genes, virus replication and protein processing. Thus these proteins are likely to have a significant impact on host physiology and metabolism. In the present study, I have examined the plant-virus interactions and the effects of three different VSRs on host physiology and gene expression levels by microarray analysis of transgenic plants that express these VSR genes. I also studied the gene expression changes related to the expression of the whole genome of Tobacco mosaic virus (TMV) in transgenic tobacco plants. Expression of the VSR genes in the transgenic tobacco plants causes significant changes in the gene expression profiles. HC-Pro gene derived from the Potyvirus Y (PVY) causes alteration of 748 and 332 transcripts, AC2 gene derived from the African cassava mosaic virus (ACMV) causes alteration of 1118 and 251transcripts, and P25 gene derived from the Potyvirus X (PVX) causes alterations of 1355 and 64 transcripts in leaves and flowers, respectively. All three VSRs cause similar up-regulation in defense, hormonally regulated and different stress-related genes and down-regulation in the photosynthesis and starch metabolism related genes. They also induce alterations that are specific to each viral VSR. The phenotype and transcriptome alterations of the HC-Pro expressing transgenic plants are similar to those observed in some Potyvirus-infected plants. The plants show increased protein degradation, which may be due to the HC-Pro cysteine endopeptidase and thioredoxin activities. The AC2-expressing transgenic plants show a similar phenotype and gene expression pattern as HC-Pro-expressing plants, but also alter pathways related to jasmonic acid, ethylene and retrograde signaling. In the P25 expressing transgenic plants, high numbers of genes (total of 1355) were up-regulated in the leaves, compared to a very low number of down-regulated genes (total of 5). Despite of strong induction of the transcripts, only mild growth reduction and no other distinct phenotype was observed in these plants. As an example of whole virus interactions with its host, I also studied gene expression changes caused by Tobacco mosaic virus (TMV) in tobacco host in three different conditions, i.e. in transgenic plants that are first resistant to the virus, and then become susceptible to it and in wild type plants naturally infected with this virus. The microarray analysis revealed up and down-regulation of 1362 and 1422 transcripts in the TMV resistant young transgenic plants, and up and down-regulation of a total of 1150 and 1200 transcripts, respectively, in the older plants, after the resistance break. Natural TMV infections in wild type plants caused up-regulation of 550 transcripts and down-regulation of 480 transcripts. 124 up-regulated and 29 down-regulated transcripts were commonly altered between young and old TMV transgenic plants, and only 6 up-regulated and none of the down-regulated transcripts were commonly altered in all three plants. During the resistant stage, the strong down-regulation in translation-related transcripts (total of 750 genes) was observed. Additionally, transcripts related to the hormones, protein degradation and defense pathways, cell division and stress were distinctly altered. All these alterations may contribute to the TMV resistance in the young transgenic plants, and the resistance may also be related to RNA silencing, despite of the low viral abundance and lack of viral siRNAs or TMV methylation activity in the plants.

Integration of Torrefaction with Steam Power Plant

Torrefaction is one of the pretreatment technologies to enhance the fuel characteristics of biomass. The efficient and continuous operation of a torrefaction reactor, in the commercial scale, demands a secure biomass supply, in addition to adequate source of heat. Biorefinery plants or biomass-fuelled steam power plants have the potential to integrate with the torrefaction reactor to exchange heat and mass, using available infrastructure and energy sources. The technical feasibility of this integration is examined in this study. A new model for the torrefaction process is introduced and verified by the available experimental data. The torrefaction model is then integrated in different steam power plants to simulate possible mass and energy exchange between the reactor and the plants. The performance of the integrated plant is investigated for different configurations and the results are compared.

Production, isolation and characterization of bioactive peptides with antihypertensive properties from rapeseed and potato protein

Consumers’ increasing awareness of healthiness and sustainability of food presents a great challenge to food industry to develop healthier, biologically active and sustainable food products. Bioactive peptides derived from food proteins are known to possess various biological activities. Among the activities, the most widely studied are antioxidant activities and angiotensin I converting enzyme (ACE) inhibitory activity related to blood pressure regulation and antihypertensive effects. Meanwhile, vast amounts of byproducts with high protein content are produced in food industry, for example potato and rapeseed industries. The utilization of these by-products could be enhanced by using them as a raw material for bioactive peptides. The objective of the present study was to investigate the production of bioactive peptides with ACE inhibitory and antioxidant properties from rapeseed and potato proteins. Enzymatic hydrolysis and fermentation were utilized for peptide production, ultrafiltration and solid-phase extraction were used to concentrate the active peptides, the peptides were fractionated with liquid chromatographic processes, and the peptides with the highest ACE inhibitory capacities were putified and analyzed with Maldi-Tof/Tof to identify the active peptide sequences. The bioavailability of the ACE inhibitory peptides was elucidated with an in vitro digestion model and the antihypertensive effects in vivo of rapeseed peptide concentrates were investigated with a preventive premise in 2K1C rats. The results showed that rapeseed and potato proteins are rich sources of ACE inhibitory and antioxidant peptides. Enzymatic hydrolysis released the peptides effectively whereas fermentation produced lower activities.The native enzymes of potato were also able to release ACE inhibitory peptides from potato proteins without the addition of exogenous enzymes. The rapeseed peptide concentrate was capable of preventing the development of hypertension in vivo in 2K1C rats, but the quality of rapeseed meal used as raw material was found to affect considerably the antihypertensive effects and the composition of the peptide fraction.

Stability of Natural Colorants of Plant Origin

In recent years, there have been studies that show a correlation between the hyperactivity of children and use of artificial food additives, including colorants. This has, in part, led to preference of natural products over products with artificial additives. Consumers have also become more aware of health issues. Natural food colorants have many bioactive functions, mainly vitamin A activity of carotenoids and antioxidativity, and therefore they could be more easily accepted by the consumers. However, natural colorant compounds are usually unstable, which restricts their usage. Microencapsulation could be one way to enhance the stability of natural colorant compounds and thus enable better usage for them as food colorants. Microencapsulation is a term used for processes in which the active material is totally enveloped in a coating or capsule, and thus it is separated and protected from the surrounding environment. In addition to protection by the capsule, microencapsulation can also be used to modify solubility and other properties of the encapsulated material, for example, to incorporate fat-soluble compounds into aqueous matrices. The aim of this thesis work was to study the stability of two natural pigments, lutein (carotenoid) and betanin (betalain), and to determine possible ways to enhance their stability with different microencapsulation techniques. Another aim was the extraction of pigments without the use of organic solvents and the development of previously used extraction methods. Stability of pigments in microencapsulated pigment preparations and model foods containing these were studied by measuring the pigment content after storage in different conditions. Preliminary studies on the bioavailability of microencapsulated pigments and sensory evaluation for consumer acceptance of model foods containing microencapsulated pigments were also carried out. Enzyme-assisted oil extraction was used to extract lutein from marigold (Tagetes erecta) flower without organic solvents, and the yield was comparable to solvent extraction of lutein from the same flowers. The effects of temperature, extraction time, and beet:water ratio on extraction efficiency of betanin from red beet (Beta vulgaris) were studied and the optimal conditions for maximum yield and maximum betanin concentration were determined. In both cases, extraction at 40 °C was better than extraction at 80 °C and the extraction for five minutes was as efficient as 15 or 30 minutes. For maximum betanin yield, the beet:water ratio of 1:2 was better, with possibly repeated extraction, but for maximum betanin concentration, a ratio of 1:1 was better. Lutein was incorporated into oil-in-water (o/w) emulsions with a polar oil fraction from oat (Avena sativa) as an emulsifier and mixtures of guar gum and xanthan gum or locust bean gum and xanthan gum as stabilizers to retard creaming. The stability of lutein in these emulsions was quite good, with 77 to 91 percent of lutein being left after storage in the dark at 20 to 22°C for 10 weeks whereas in spray dried emulsions the retention of lutein was 67 to 75 percent. The retention of lutein in oil was also good at 85 percent. Betanin was incorporated into the inner w1 water phase of a water1-in-oil-inwater2 (w1/o/w2) double emulsion with primary w1/o emulsion droplet size of 0.34 μm and secondary w1/o/w2 emulsion droplet size of 5.5 μm and encapsulation efficiency of betanin of 89 percent. In vitro intestinal lipid digestion was performed on the double emulsion, and during the first two hours, coalescence of the inner water phase droplets was observed, and the sizes of the double emulsion droplets increased quickly because of aggregation. This period also corresponded to gradual release of betanin, with a final release of 35 percent. The double emulsion structure was retained throughout the three-hour experiment. Betanin was also spray dried and incorporated into model juices with different pH and dry matter content. Model juices were stored in the dark at -20, 4, 20–24 or 60 °C (accelerated test) for several months. Betanin degraded quite rapidly in all of the samples and higher temperature and a lower pH accelerated degradation. Stability of betanin was much better in the spray dried powder, with practically no degradation during six months of storage in the dark at 20 to 24 °C and good stability also for six months in the dark at 60 °C with 60 percent retention. Consumer acceptance of model juices colored with spray dried betanin was compared with similar model juices colored with anthocyanins or beet extract. Consumers preferred beet extract and anthocyanin colored model juices over juices colored with spray dried betanin. However, spray dried betanin did not impart any off-odors or off-flavors into the model juices contrary to the beet extract. In conclusion, this thesis describes novel solvent-free extraction and encapsulation processes for lutein and betanin from plant sources. Lutein showed good stability in oil and in o/w emulsions, but slightly inferior in spray dried emulsions. In vitro intestinal lipid digestion showed a good stability of w1/o/w2 double emulsion and quite high retention of betanin during digestion. Consumer acceptance of model juices colored with spray dried betanin was not as good as model juices colored with anthocyanins, but addition of betanin to real berry juice could produce better results with mixture of added betanin and natural berry anthocyanins could produce a more acceptable color. Overall, further studies are needed to obtain natural colorants with good stability for the use in food products.

From protein structure to function with bioinformatics

It has long been known that amino acids are the building blocks for proteins and govern their folding into specific three-dimensional structures. However, the details of this process are still unknown and represent one of the main problems in structural bioinformatics, which is a highly active research area with the focus on the prediction of three-dimensional structure and its relationship to protein function. The protein structure prediction procedure encompasses several different steps from searches and analyses of sequences and structures, through sequence alignment to the creation of the structural model. Careful evaluation and analysis ultimately results in a hypothetical structure, which can be used to study biological phenomena in, for example, research at the molecular level, biotechnology and especially in drug discovery and development. In this thesis, the structures of five proteins were modeled with templatebased methods, which use proteins with known structures (templates) to model related or structurally similar proteins. The resulting models were an important asset for the interpretation and explanation of biological phenomena, such as amino acids and interaction networks that are essential for the function and/or ligand specificity of the studied proteins. The five proteins represent different case studies with their own challenges like varying template availability, which resulted in a different structure prediction process. This thesis presents the techniques and considerations, which should be taken into account in the modeling procedure to overcome limitations and produce a hypothetical and reliable three-dimensional structure. As each project shows, the reliability is highly dependent on the extensive incorporation of experimental data or known literature and, although experimental verification of in silico results is always desirable to increase the reliability, the presented projects show that also the experimental studies can greatly benefit from structural models. With the help of in silico studies, the experiments can be targeted and precisely designed, thereby saving both money and time. As the programs used in structural bioinformatics are constantly improved and the range of templates increases through structural genomics efforts, the mutual benefits between in silico and experimental studies become even more prominent. Hence, reliable models for protein three-dimensional structures achieved through careful planning and thoughtful executions are, and will continue to be, valuable and indispensable sources for structural information to be combined with functional data.