Stereochemistry of collagen

This review article, based on a lecture delivered in Madras in 1985, is an account of the author's experience in the working out of the molecular structure and conformation of the collagen triple-helix over the years 1952–78. It starts with the first proposal of the correct triple-helix in 1954, but with three residues per turn, which was later refined in 1955 into a coiled-coil structure with approximately 3.3 residues per turn. The structure readily fitted proline and hydroxyproline residues and required glycine as every third residue in each of the three chains. The controversy regarding the number of hydrogen bonds per tripeptide could not be resolved by X-ray diffraction or energy minimization, but physicochemical data, obtained in other laboratories during 1961–65, strongly pointed to two hydrogen bonds, as suggested by the author. However, it was felt that the structure with one straight NH … O bond was better. A reconciliation of the two was obtained in Chicago in 1968, by showing that the second hydrogen bond is via a water molecule, which makes it weaker, as found in the physicochemical studies mentioned above. This water molecule was also shown, in 1973, to take part in further cross-linking hydrogen bonds with the OH group of hydroxyproline, which occurred always in the location previous to glycine, and is at the right distance from the water. Thus, almost all features of the primary structure, X-ray pattern, optical and hydrodynamic data, and the role of hydroxyproline in stabilising the triple helical structure, have been satisfactorily accounted for. These also lead to a confirmation of Pauling's theory that vitamin C improves immunity to diseases, as explained in the last section.

Comparative measurements of HV impulses to evaluate different sets of response parameters

Results are reported of comparative measurements made in 14 HV (high-voltage) laboratories in ten different countries. The theory of the proposed methods of characterizing the dynamic behavior is given, and the parameters to be used are discussed. Comparative measurements made using 95 systems based on 53 dividers are analyzed. This analysis shows that many of the system now in use, even though they fulfil the basic response requirements of the standards, do not meet the accuracy requirements. Because no transfer measurements were made between laboratories, there is no way to detect similar errors in both the system under test and the reference system. Hence, the situation may be worse than reported. This has led to the recommendation that comparative measurements should be the main route for quantifying industrial impulse measuring systems

Helsingin Östersundomin pienvesien kartoitus

The area of Östersundom (29,1 square kilometers) was attached to Helsinki in the beginning of the year 2009. Östersundom is formed mostly from the municipality of Sipoo, and partly from the city of Vantaa. Nowadays Östersundom is still quite rural, but city planning has already started, and there are plans to develop Östersundom into a district with 45 000 inhabitants. In this study, the headwaters, streams and small lakes of Östersundom were studied to produce information as a basis for city planning. There are six main streams and five small lakes in Östersundom. The main methodology used in this study was the examination of the physical and the chemical quality of the water. The hygienic quality of the water was also studied. It was also examined whether the waters are in their natural state, or have they been treated and transformed by man. In addition, other factors affecting the waters were examined. Geographical information data was produced as a result of this work. Östersundom is the main area looked at in this study, some factors are examined in the scope of the catchment areas. Water samples were collected in three sampling periods: 31.8 4.9.2009, 3. 4.2.2010, and 10. 14.4.2010. There were 20 sampling points in Östersundom (5 in small lakes, 15 in streams). In the winter sampling period, only six samples were collected, from which one was taken from a small lake. Field measurements associated with water sampling included water temperature, oxygen concentration, pH and electoral conductivity. Water samples were analyzed in the Laboratories of Physical Geography in the University of Helsinki for the following properties: total suspended solids (TSS), total dissolved substances (TDS), organic matter, alkalinity, colour, principal anions and cations and trace elements. Metropolilab analyzed the amount of faecal coliform bacteria in the samples. The waters in Östersundom can be divided to three classes according to water quality and other characteristics: the upper course of the streams, the lower course of the streams and the small lakes. The streams in their upper course are in general acidic, and their acid neutralization capacity is low. The proportion of the organic matter is high. Also the concentrations of aluminium and iron tend to be high. The streams in the lower course have acidity closer to neutral, and the buffering capacity is good. The amounts of TSS and TDS are high, and as a result, the concentrations of many ions and trace elements are high as well. Bacteria were detected at times in the streams of the lower course. Four of the five small lakes in Östersundom are humic and acidic. TSS and TDS concentrations tend to be low, but the proportion of organic matter is often high. There were no bacteria in the small lakes. The fifth small lake (Landbonlampi) differs from the others by its water colour, which is very clear. This lake is very acidic, and its buffering capacity is extremely low. Compared to the headwaters in Finland in general, the concentrations of many ions and trace elements are higher in Östersundom. On the other hand, the characteristics of water were different according to the classification upper course streams, lower course streams, and small lakes. Generally, the best water quality was observed in the stream of Gumbölenpuro and in the lakes Storträsk, Genaträsk, Hältingträsk and Landbonlampi. Several valuable waters in their natural state were discovered from the area. The most representative example is the stream of Östersundominpuro in its lower course, where the stream flows through a broad-leaf forest area. The small lakes of Östersundom, and the biggest stream Krapuoja, with its meandering channel, are also valuable in their natural state.

Accurate mass-based analysis in human sport doping control : Application of liquid chromatography - time-of-flight mass spectrometry

Human sport doping control analysis is a complex and challenging task for anti-doping laboratories. The List of Prohibited Substances and Methods, updated annually by World Anti-Doping Agency (WADA), consists of hundreds of chemically and pharmacologically different low and high molecular weight compounds. This poses a considerable challenge for laboratories to analyze for them all in a limited amount of time from a limited sample aliquot. The continuous expansion of the Prohibited List obliges laboratories to keep their analytical methods updated and to research new available methodologies. In this thesis, an accurate mass-based analysis employing liquid chromatography - time-of-flight mass spectrometry (LC-TOFMS) was developed and validated to improve the power of doping control analysis. New analytical methods were developed utilizing the high mass accuracy and high information content obtained by TOFMS to generate comprehensive and generic screening procedures. The suitability of LC-TOFMS for comprehensive screening was demonstrated for the first time in the field with mass accuracies better than 1 mDa. Further attention was given to generic sample preparation, an essential part of screening analysis, to rationalize the whole work flow and minimize the need for several separate sample preparation methods. Utilizing both positive and negative ionization allowed the detection of almost 200 prohibited substances. Automatic data processing produced a Microsoft Excel based report highlighting the entries fulfilling the criteria of the reverse data base search (retention time (RT), mass accuracy, isotope match). The quantitative performance of LC-TOFMS was demonstrated with morphine, codeine and their intact glucuronide conjugates. After a straightforward sample preparation the compounds were analyzed directly without the need for hydrolysis, solvent transfer, evaporation or reconstitution. The hydrophilic interaction technique (HILIC) provided good chromatographic separation, which was critical for the morphine glucuronide isomers. A wide linear range (50-5000 ng/ml) with good precision (RSD<10%) and accuracy (±10%) was obtained, showing comparable or better performance to other methods used. In-source collision-induced dissociation (ISCID) allowed confirmation analysis with three diagnostic ions with a median mass accuracy of 1.08 mDa and repeatable ion ratios fulfilling WADA s identification criteria. The suitability of LC-TOFMS for screening of high molecular weight doping agents was demonstrated with plasma volume expanders (PVE), namely dextran and hydroxyethylstarch (HES). Specificity of the assay was improved, since interfering matrix compounds were removed by size exclusion chromatography (SEC). ISCID produced three characteristic ions with an excellent mean mass accuracy of 0.82 mDa at physiological concentration levels. In summary, by combining TOFMS with a proper sample preparation and chromatographic separation, the technique can be utilized extensively in doping control laboratories for comprehensive screening of chemically different low and high molecular weight compounds, for quantification of threshold substances and even for confirmation. LC-TOFMS rationalized the work flow in doping control laboratories by simplifying the screening scheme, expediting reporting and minimizing the analysis costs. Therefore LC-TOFMS can be exploited widely in doping control, and the need for several separate analysis techniques is reduced.

Genomic alterations in Myeloproliferative Neoplasms and Myelodysplastic Syndromes

Myeloproliferative neoplasms (MPN) and myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic disorders whose etiology and molecular pathogenesis are poorly understood. During the past decade, enormous developments in microarray technology and bioinformatics methods have made it possible to mine novel molecular alterations in a large number of malignancies, including MPN and MDS, which has facilitated the detection of new prognostic, predictive and therapeutic biomarkers for disease stratification. By applying novel microarray techniques, we profiled copy number alterations and microRNA (miRNA) expression changes in bone marrow aspirate and blood samples. In addition, we set up and validated an miRNA expression test for bone marrow core biopsies in order to utilize the large archive material available in many laboratories. We also tested JAK2 mutation status and compare it with the in vitro growth pattern of hematologic progenitors cells. In the study focusing on 100 MPN cases, we detected a Janus kinase 2 (JAK2) mutation in 71 cases. We observed spontaneous erythroid colony growth in all mutation-positive cases in addition to nine mutation negative cases. Interestingly, seven JAK2V167F negative ET cases showed spontaneous megakaryocyte colony formation, one case of which also harbored a myeloproliferative leukemia virus oncogene (MPL) mutation. We studied copy number alterations in 35 MPN and 37 MDS cases by using oligonucleotide-based array comparative hybridization (array CGH). Only one essential thrombocythemia (ET) case presented copy number alterations in chromosomes 1q and 13q. In contrast, MDS cases were characterized by numerous novel cryptic chromosomal aberrations with the most common copy number losses at 5q21.3q33.1 and 7q22.1q33, while the most common copy number gain was trisomy 8. As for the study of the bone marrow core biopsy samples, we showed that even though these samples were embedded in paraffin and underwent decalcification, they were reliable sources of miRNA and suitable for array expression analysis. Further, when studying the miRNA expression profiles of the 19 MDS cases, we found that, compared to controls, two miRNAs (one human Epstein-Barr virus (miR-BART13) miRNA and one human (has-miR-671-5p) miRNA) were downregulated, whereas two other miRNAs (hsa-miR-720 and hsa-miR-21) were upregulated. However, we could find no correlation between copy number alterations and microRNA expression when integrating these two data. This thesis brings to light new information about genomic changes implicated in the development of MPN and MDS, and also underlines the power of applying genome-wide array screening techniques in neoplasias. Rapid advances in molecular techniques and the integration of different genomic data will enable the discovery of the biological contexts of many complex disorders, including myeloid neoplasias.

Evaluation of Erosion Resistance of Metallic Materials and the Role of Material Properties in Correlations

A study of the correlations between material properties and normalized erosion resistance (inverse of erosion rates) of various materials tested in the rotating disk and the flow venturi at various intensities indicates that different individual properties influence different stages of erosion. At high and low intensities of erosion, energy properties predominate the phenomenon, whereas at intermediate intensities strength and acoustic properties become more significant. However, both strength and energy properties are significant in the correlations for the entire spectrum of erosion when extensive cavitation and liquid impingement data from several laboratories involving different intensities and hydrodynamic conditions are considered. The use of true material properties improved the statistical parameters by 3 to 37%, depending on the intensity of erosion. It is possible to evaluate qualitatively the erosion resistances of materials based on the true stress-true strain curves.

Development of radiosynthesis methods for 18F-labelled radiopharmaceuticals : General considerations and production of a dopamine transporter radioligand

Positron emission tomography (PET) is a molecular imaging technique that utilises radiopharmaceuticals (radiotracers) labelled with a positron-emitting radionuclide, such as fluorine-18 (18F). Development of a new radiotracer requires an appropriate radiosynthesis method: the most common of which with 18F is nucleophilic substitution with [18F]fluoride ion. The success of the labelling reaction is dependent on various factors such as the reactivity of [18F]fluoride, the structure of the target compound in addition to the chosen solvent. The overall radiosynthesis procedure must be optimised in terms of radiochemical yield and quality of the final product. Therefore, both quantitative and qualitative radioanalytical methods are essential in developing radiosynthesis methods. Furthermore, biological properties of the tracer candidate need to be evaluated by various pre-clinical studies in animal models. In this work, the feasibility of various nucleophilic 18F-fluorination strategies were studied and a labelling method for a novel radiotracer, N-3-[18F]fluoropropyl-2beta-carbomethoxy-3beta-4-fluorophenyl)nortropane ([18F]beta-CFT-FP), was optimised. The effect of solvent was studied by labelling a series of model compounds, 4-(R1-methyl)benzyl R2-benzoates. 18F-Fluorination reactions were carried out both in polar aprotic and protic solvents (tertiary alcohols). Assessment of the 18F-fluorinated products was studied by mass spectrometry (MS) in addition to conventional radiochromatographic methods, using radiosynthesis of 4-[18F]fluoro-N-[2-[1-(2-methoxyphenyl)-1-piperazinyl]ethyl-N-2-pyridinyl-benzamide (p-[18F]MPPF) as a model reaction. Labelling of [18F]beta-CFT-FP was studied using two 18F-fluoroalkylation reagents, [18F]fluoropropyl bromide and [18F]fluoropropyl tosylate, as well as by direct 18F-fluorination of sulfonate ester precursor. Subsequently, the suitability of [18F]beta-CFT-FP for imaging dopamine transporter (DAT) was evaluated by determining its biodistribution in rats. The results showed that protic solvents can be useful co-solvents in aliphatic 18F-fluorinations, especially in the labelling of sulfonate esters. Aromatic 18F-fluorination was not promoted in tert-alcohols. Sensitivity of the ion trap MS was sufficient for the qualitative analysis of the 18F-labelled products; p-[18F]MPPF was identified from the isolated product fraction with a mass-to-charge (m/z) ratio of 435 (i.e. protonated molecule [M+H]+). [18F]beta-CFT-FP was produced most efficiently via [18F]fluoropropyl tosylate, leading to sufficient radiochemical yield and specific radioactivity for PET studies. The ex vivo studies in rats showed fast kinetics as well as the specific uptake of [18F]beta-CFT-FP to the DAT rich brain regions. Thus, it was concluded that [18F]beta-CFT-FP has potential as a radiotracer for imaging DAT by PET.

Microbial identification by detection of ligation probes on DNA microarray

Microbes in natural and artificial environments as well as in the human body are a key part of the functional properties of these complex systems. The presence or absence of certain microbial taxa is a correlate of functional status like risk of disease or course of metabolic processes of a microbial community. As microbes are highly diverse and mostly notcultivable, molecular markers like gene sequences are a potential basis for detection and identification of key types. The goal of this thesis was to study molecular methods for identification of microbial DNA in order to develop a tool for analysis of environmental and clinical DNA samples. Particular emphasis was placed on specificity of detection which is a major challenge when analyzing complex microbial communities. The approach taken in this study was the application and optimization of enzymatic ligation of DNA probes coupled with microarray read-out for high-throughput microbial profiling. The results show that fungal phylotypes and human papillomavirus genotypes could be accurately identified from pools of PCR amplicons generated from purified sample DNA. Approximately 1 ng/μl of sample DNA was needed for representative PCR amplification as measured by comparisons between clone sequencing and microarray. A minimum of 0,25 amol/μl of PCR amplicons was detectable from amongst 5 ng/μl of background DNA, suggesting that the detection limit of the test comprising of ligation reaction followed by microarray read-out was approximately 0,04%. Detection from sample DNA directly was shown to be feasible with probes forming a circular molecule upon ligation followed by PCR amplification of the probe. In this approach, the minimum detectable relative amount of target genome was found to be 1% of all genomes in the sample as estimated from 454 deep sequencing results. Signal-to-noise of contact printed microarrays could be improved by using an internal microarray hybridization control oligonucleotide probe together with a computational algorithm. The algorithm was based on identification of a bias in the microarray data and correction of the bias as shown by simulated and real data. The results further suggest semiquantitative detection to be possible by ligation detection, allowing estimation of target abundance in a sample. However, in practise, comprehensive sequence information of full length rRNA genes is needed to support probe design with complex samples. This study shows that DNA microarray has the potential for an accurate microbial diagnostic platform to take advantage of increasing sequence data and to replace traditional, less efficient methods that still dominate routine testing in laboratories. The data suggests that ligation reaction based microarray assay can be optimized to a degree that allows good signal-tonoise and semiquantitative detection.

Molecular diagnosis of developmental disorders

ABSTRACT Idiopathic developmental disorders (DDs) affect ~1% of the population worldwide. This being a considerable amount, efforts are being made to elucidate the disease mechanisms. One or several genetic factors cause 30-40% of DDs, and only 10% are caused by environmental factors. The remaining 50% of DD patients go undiagnosed, mostly due to a lack of diagnostic techniques. The cause in most undiagnosed cases is though to be a genetic factor or a combination of genetic and environmental factors. Despite the surge of new technologies entering the market, their implementation into diagnostic laboratories is hampered by costs, lack of information about the expected diagnostic yield, and the wide range of selection. This study evaluates new microarray methods in diagnosing idiopathic DDs, providing information about their added diagnostic value. Study I analysed 150 patients by array comparative genomic hybridization (array CGH, 44K and 244K), with a subsequent 18% diagnostic yield. These results are supported by other studies, indicating an enourmous added diagnostic value of array CGH, compared with conventional cytogenetic analysis. Nevertheless, 80% of the patients remained undiagnosed in Study I. In an effort to diagnose more patients, in Study IV the resolution was increased from 8.9 Kb of the 244K CGH array to 0.7 Kb, by using a single-nucleotide polymorphism (SNP) array. However, no additional pathogenic changes were detected in the 35 patients assessed, and thus, for diagnostic purposes, an array platform with ca 9 Kb resolution appears adequate. The recent vast increase in reports of detected aberrations and associated phenotypes has enabled characterization of several new syndromes first based on a common aberration and thereafter by delineation of common clinical characteristics. In Study II, a familial deletion at 9q22.2q22.32 with variable penetrance was described. Despite several reports of aberrations in the adjacent area at 9q associated with Gorlin syndrome, the patients in this family had a unique phenotype and did not present with the syndrome. In Study III, a familial duplication of chromosome 6p22.2 was described. The duplication caused increased expression of an important enzyme of the γ-aminobutyric acid (GABA) degradation pathway, causing oxidative stress of the brain, and thus, very likely, the mild mental retardation of these patients. These two case studies attempted to pinpoint candidate genes and to resolve the pathogenic mechanism causing the clinical characteristics of the patients. Presenting rare genetic and clinical findings to the international science and medical community enables interpretation of similar findings in other patients. The added value of molecular karyotyping in patients with idiopathic DD is evident. As a first line of testing, arrays with a median resolution of at least 9 Kb should be considered and further characterization of detected aberrations undertaken when possible. Diagnostic whole-exome sequencing may be the best option for patients who remain undiagnosed after high-resolution array analysis.

Si, Si-Ge and the new heterostructure world

Semiconductor heterostructures based on AlAs/GaAs and other III-V compounds have been the focus of active research for some time now. Ih the last decade, a new heterostructure material, the strained Si/SiGe system, has emerged. This heterojunction technology can potentially be integrated into the current VLSI environment with large-scale impact in the growing microelectronics market. Si/SiGe heterojunction bipolar transistors with cut-off frequencies exceeding 100 GHz and other electronic and optical devices with superior properties compared to all-Si technology have been demonstrated in laboratories worldwide.

Robust controller for an autonomous small refrigeration unit

The authors describe the constructional features of a controller for operating an autonomous refrigeration unit powered by a field of photovoltaic panels and backed up by a generator set. The controller enables three voltage levels of operation of an inverter to meet the start, run and off cycle conditions of the refrigerator compressor. The algorithm considers several input and output parameters and status signals from each subsystem of the unit to deduce a control strategy. Such units find application for storage of vaccines and life-saving medicines requiring uninterrupted refrigeration, in medical shops, rural health centres, veterinary laboratories etc.

Novel phase-transition behavior near liquid/liquid critical points of aqueous solutions: Formation of a third phase at the interface

We report a novel phase behavior in aqueous solutions of simple organic solutes near their liquid/liquid critical points, where a solid-like third phase appears at the liquid/liquid interface. The phenomenon has been found in three different laboratories. It appears in many aqueous systems of organic solutes and becomes enhanced upon the addition of salt to these solutions.

The effect of particle size on performance of cathode materials of Li-ion batteries

Beginning with the ‘frog-leg experiment’ by Galvani (1786), followed by the demonstrations of Volta pile by Volta (1792) and lead-acid accumulator by Plante´ (1859), several battery chemistries have been developed and realized commercially. The development of lithium-ion rechargeable battery in the early 1990s is a breakthrough in the science and technology of batteries. Owing to its high energy density and high operating voltage, the Li-ion battery has become the battery of choice for various portable applications such as note-book computers, cellular telephones, camcorders, etc. Huge efforts are underway in succeeding the development of large size batteries for electric vehicle applications. The origin of lithium-ion battery lies in the discovery that Li+-ions can reversibly be intercalated into/de-intercalated from the Van der Walls gap between graphene sheets of carbon materials at a potential close to the Li/Li+ electrode. By employing carbon as the negative electrode material in rechargeable lithium-ion batteries, the problems associated with metallic lithium in rechargeable lithium batteries have been mitigated. Complimentary investigations on intercalation compounds based on transition metals have resulted in establishing LiCoO2 as the promising cathode material. By employing carbon and LiCoO2, respectively, as the negative and positive electrodes in a non-aqueous lithium-salt electrolyte,a Li-ion cell with a voltage value of about 3.5 V has resulted.Subsequent to commercialization of Li-ion batteries, a number of research activities concerning various aspects of the battery components began in several laboratories across the globe. Regarding the positive electrode materials, research priorities have been to develop different kinds of active materials concerning various aspects such as safety, high capacity, low cost, high stability with long cycle-life, environmental compatibility,understanding relationships between crystallographic and electrochemical properties. The present review discusses the published literature on different positive electrode materials of Li-ion batteries, with a focus on the effect of particle size on electrochemical performance.

Bactericidal/permeability increasing protein: A multifaceted protein with functions beyond LPS neutralization

Bactericidal permeability increasing protein (BPI), a 55-60kDa protein, first reported in 1975, has gone a long way as a protein with multifunctional roles. Its classical role in neutralizing endotoxin (LPS) raised high hopes among septic shock patients. Today, BPI is not just a LPS-neutralizing protein, but a protein with diverse functions. These functions can be as varied as inhibition of endothelial cell growth and inhibition of dendritic cell maturation, or as an anti-angiogenic, chemoattractant or opsonization agent. Though the literature available is extremely limited, it is fascinating to look into how BPI is gaining major importance as a signalling molecule. In this review, we briefly summarize the recent research focused on the multiple roles of BPI and its use as a therapeutic.

Nanocomposite based flexible ultrasensitive resistive gas sensor for chemical reactions studies

Room temperature operation, low detection limit and fast response time are highly desirable for a wide range of gas sensing applications. However, the available gas sensors suffer mainly from high temperature operation or external stimulation for response/recovery. Here, we report an ultrasensitive-flexible-silver-nanoparticle based nanocomposite resistive sensor for ammonia detection and established the sensing mechanism. We show that the nanocomposite can detect ammonia as low as 500 parts-per-trillion at room temperature in a minute time. Furthermore, the evolution of ammonia from different chemical reactions has been demonstrated using the nanocomposite sensor as an example. Our results demonstrate the proof-of-concept for the new detector to be used in several applications including homeland security, environmental pollution and leak detection in research laboratories and many others.