Long sequence duplications, repeats, and palindromes in HIV-1 gp120: length variation in V4 as the product of misalignment mechanism.

We have shown that indels in gp120 V4 are associated to the presence of duplicated and palindromic sequences, suggesting that they may be produced by strand-slippage misalignment mechanism. Indels in V4 involved region-specific duplications 9 to 15 bp long, and repeats of various lengths, associated to trinucleotides AAT. No duplications were found in V3 and C3. The frequency of palindromic sequences in individual genes was found to be significantly higher in gp120 (p < or = 3.00E-7), and significantly lower in Tat (p < or = 9.00E-7) than the average frequency calculated over the full genome. The finding of elements of misalignment in association with indels in V4 suggests that these mutations may occur in proviral DNA after integration of HIV into the host genome. It also implies that occurrence of large indels in gp120 is not random but is directed by the presence and distribution of elements of misalignment in the HIV genome.

Growth rate and wood properties of Norway spruce cutting clones on different sites

[Abstract]

Leaf-cutting ant attack in initial pine plantations and growth of defoliated plants

The objective of this work was to evaluate the natural attack by Acromyrmex crassispinus in initial Pinus taeda plantations without control measures against ants, as well as the effect of defoliation in seedlings of P. taeda. Evaluations of the attack of leaf-cutting ants on P. taeda plantations were done monthly in the first six months, then 9 and 12 months after planting. The percentages of plants that were naturally attacked by ants were registered. The effect of defoliation was evaluated by artificial defoliation, simulating the natural patterns of attack by A. crassispinus on P. taeda seedlings. The natural attack of A. crassispinus was greater during the first months after planting, being more intense in the first 30 days. Artificial defoliation indicated that there were no significant losses in diameter and height in plants with less than 75% defoliation. However, there were significant losses in diameter and height in plants with 100% defoliation, independently of the cut of the apical meristem, and also plant death. The control of leaf-cutting ants in P. taeda plantings, in which A. crassispinus is the most frequent leaf-cutting ant, should be intense only at the beginning of planting, since the most severe attacks occur during this time.

Length variation in HIV-1 gp120 as the product of DNA misalignment mechanism

Background: To determine whether misalignment structures such as duplications, repeats, and palindromes are associated to insertions/deletions (indels) in gp120, indicating that indels are indeed frameshift mutations generated by DNA misalignment mechanism. Methods: Cloning and sequencing of a fragment of HIV-1 gp120 spanning C2-C4 derived from plasma RNA in 12 patients with early chronic disease and naïve to antiretroviral therapy. Results: Indels in V4 involved always insertion and deletion of duplicated nucleotide segments, and AAT repeats, and were associated to the presence of palindromic sequences. No duplications were detected in V3 and C3. Palindromic sequences occurred with similar frequencies in V3, C3 and V4; the frequency of palindromes in individual genes was found to be significantly higher in structural (gp120, p ≤ 3.00E-7) and significantly lower in regulatory (Tat, p ≤ 9.00E-7) genes, as compared to the average frequency calculated over the full genome. Discussion: Indels in V4 are associated to misalignment structures (i.e. duplications repeat and palindromes) indicating DNA misalignment as the mechanism underlying length variation in V4. The finding that indels in V4 are caused by DNA misalignment has some very important implications: 1) indels in V4 are likely to occur in proviral DNA (and not in RNA), after integration of HIV into the host genome; 2) they are likely to occur as progressive modifications of the early founder virus during chronic infection, as more and more cells get infected; 3) frameshift mutations involving any number of base pairs are likely to occur evenly across gp120; however, only those mutants carrying a functional gp120 (indels as multiples of three base pairs) will be able to perpetuate the virus cycle and to keep spreading through the population.

Cutting edge: stimulation with the cognate self-antigen induces expression of the Ly49A receptor on self-reactive T cells which modulates their responsiveness.

NK cell self-tolerance is maintained by inhibitory receptors specific for MHC class I molecules. Inhibitory NK receptors are also expressed on memory CD8 T cells but their biological relevance on T cells is unclear. In this study, we describe the expression of the Ly49A receptor on a subset of autoreactive T cells which persist in mice double-transgenic for the lymphocytic choriomeningitis virus-derived peptide gp33 and a TCRalphabeta specific for the gp33. No Ly49A-expressing cells are found in TCRalphabeta single-transgenic mice, indicating that the presence of the autoantigen is required for Ly49A induction. Direct evidence for an Ag-specific initiation of Ly49A expression has been obtained in vitro after stimulation of autoreactive TCRalphabeta T cells with the cognate self-Ag. This expression of Ly49A substantially reduces Ag-specific activation of autoreactive T cells. These findings thus suggest that autoantigen-specific induction of inhibitory NK cell receptors on T cells may contribute to peripheral self-tolerance.

Tumor sensitizing function and mechanism of action of a RasGAP derived peptide

Cancer is the second cause of death after cardio-vascular diseases in economically developed countries. Two of the most commonly used anti-cancer therapies are chemo and radiotherapy. Despite the remarkable advances made in term of delivery and specificity of these two anti-tumor regimens, their toxicity towards healthy tissue remains a limitation. A promising approach to overcome this obstacle would be the utilization of therapeutic peptides that specifically augment the sensitivity of tumoral cells to treatments. Lower therapeutical doses would then be required to kill malignant cells, limiting toxic effects on healthy tissues. It was previously shown in our laboratory that the caspase-3 generated fragment N2 of RasGAP is able to potentiate the genotoxin-induced apoptosis selectively in cancer cells. In this work we show that fragment N2 strictly requires a cytoplasmic localization to deliver its pro-apoptotic effect in genotoxin-treated cancer cells. The tumor sensitizing capacity of fragment N2 was found to reside within the 10 amino acid sequence 317-326. Our laboratory earlier demonstrated that a peptide corresponding to amino acids 317 to 326 of RasGAP fused to the TAT cell permeable moiety, called TAT-RasGAP317.326, is able to sensitize cancer cells, but not normal cells, to genotoxin-induced apoptosis. In the present study we describe the capacity of TAT-RasGAP 317.326 to sensitize tumors to both chemo and radiotherapy in an in vivo mouse model. The molecular mechanism underlying the TAT-RasGAP 317.326-mediated sensitization starts now to be elucidated. We demonstrate that G3BP1, an endoribonuclease binding to amino acids 317-326 of RasGAP, is not involved in the sensitization mechanism. We also provide evidence showing that TAT-RasGAP3 17-326 potentiates the genotoxin-mediated activation of Bax in a tBid-dependent manner. Altogether our results show that TAT-RasGAP 317.326 could be potentially used in cancer therapy as sensitizer, in order to improve the efficacy of chemo and radiotherapy and prolong the life expectancy of cancer patients. Moreover, the understanding of the TAT-RasGAP317.326 mode of action might help to unravel the mechanisms by which cancer cells resist to chemo and radiotherapy and therefore to design more targeted and efficient anti-tumoral strategies.

Market potentialfor free-cutting steels in Europe

Työn tavoitteena oli selvittää tilannetta Euroopan automaattiteräsmarkkinoilla ja sen perusteella arvioida Imatra Steelin mahdollisuuksia kilpailla kyseessä olevilla markkinoilla. Tärkein tavoite oli kokonaismarkkinapotentiaalin arvioiminen Saksan, Ruotsin, Englannin ja Suomen markkinoilla. Lisäksi selvitettiin käytetyt automaattiteräslajit ja mitta-alue, hintataso sekä koneistukseenliittyviä teknisiä yksityiskohtia.Tavoitteena oli myös kartoittaa asenteita ja mielipiteitä mahdollisesta lyijyn käytön kieltämisestä teräksen seosaineena tulevaisuudessa. Paremman kokonaiskuvan saamiseksi analysoitiin myös kilpailutilannetta Euroopassa. Työn teoriakehyksessä tutkittiin teollisuustuotteiden markkinatutkimuksen suorittamisen erityispiirteitä, markkinapotentiaalin määrittämiseen liittyviä käsitteitä ja kilpailija-analyysin suorittamista. Empiirinen tutkimus suoritettiin pääasiassa asiantuntijoiden haastattelujen ja kyselyjen avulla. Haastateltavina oli tukkureita ja loppukäyttäjiä. Kilpailutilanteen kartoittaminen perustuu lähinnä sekundääriseen tietoon, Internet-sivuihin ja myyntikonttoreiden aikaisemmin keräämään tietoon.Automaattiterästen kokonaispotentiaaliksi Euroopassa arvioitiin miljoona tonnia ja suurin osa kaupasta käydään tutkituilla markkina-alueilla. Suurimmat volyymit sijoittuvat pienemmille mitta-alueille, Æ 12 - 50 mm. Markkinoita hallitsee muutama suuri teräksen valmistaja. Imatra Steel kohtuullisen pienenä toimittajana ei pysty kilpailemaan volyymilla ja tuotevalikoimallaan suurten teräsjättien kanssa. Imatra Steelin mahdollinen strategiavaihtoehto olisi yrittää löytää ne kapeat segmentit ja markkinaraot, joilla sen tuotteet jatietotaito tuovat asiakkaalle suurimman mahdollisen hyödyn verrattuna kilpailijoihin.

CO2 Laser Cutting of Particleboard, HDF and MDF

The purpose of this thesis is to reveal how the laser cutting parameters influence lasercutting of particleboard, HDF and MDF. The literature review introduces the basic principle of CO2 laser, CO2 laser equipment and its usage in cutting of wood-based materials. The experimental part focuses on the discussion and analysis ofthe test data and attempts to draw conclusions on the influence of various parameters, including laser power, focal length of the lens and cutting gas, on the cutting speed and kerf quality. The tested materials include various thicknesses of particleboard, HDF and MDF samples. A TRUMPF TLF2700 HQ laser equipment was used for the experiments. To obtain valid data, the test samples must be completely cut through without any bonding of wood fibre. The maximum cutting speed is linear dependent on the laser power in thecondition that the other parameters are constant. For each thickness of a specific material type, there is a minimum laser power for cutting. Normally, the topand bottom kerf widths increase with the enhancement of laser power. There may be a critical laser power which can generate the minimum cross-sectional kerf width. Lens of larger focal length may achieve higher cutting speed. As the focal length becomes larger, the top kerf width tends to increase while the bottom andcross-sectional kerf widths to the opposite. Of all cutting gases, oxygen can help achieve higher cutting speed. The gas pressure of nitrogen does not seem to have strong influence on the cutting result. Generally, 2 bar air is more preferable for higher cutting speed. For particleboard and MDF samples of larger thickness than 12 mm, 2 bar argon can be used to reach remarkably higher cutting speed than the 5 bar. Generally, the 190.5 mm lens can produce smallest total kerf width. The kerf sides of thicker samples are darker than the thinner ones. The sample darkness tends to be lower as laser power increased. 63.5 mm lens seemed tocause more darkness than other lens. 5 bar cutting gases can produce less dark side kerfs than 2 bar ones. Oxygen normally causes darker kerfs than other gases. No distinct differences were found between nitrogen and argon.

Laser Cutting of Austenitic Stainless Steel with a High Quality Laser Beam

The thin disk and fiber lasers are new solid-state laser technologies that offer a combinationof high beam quality and a wavelength that is easily absorbed by metal surfacesand are expected to challenge the CO2 and Nd:YAG lasers in cutting of metals ofthick sections (thickness greater than 2mm). This thesis studied the potential of the disk and fiber lasers for cutting applications and the benefits of their better beam quality. The literature review covered the principles of the disk laser, high power fiber laser, CO2 laser and Nd:YAG laser as well as the principle of laser cutting. The cutting experiments were made with thedisk, fiber and CO2 lasers using nitrogen as an assist gas. The test material was austenitic stainless steel of sheet thickness 1.3mm, 2.3mm, 4.3mm and 6.2mm for the disk and fiber laser cutting experiments and sheet thickness of 1.3mm, 1.85mm, 4.4mm and 6.4mm for the CO2 laser cutting experiments. The experiments focused on the maximum cutting speeds with appropriate cut quality. Kerf width, cutedge perpendicularity and surface roughness were the cut characteristics used to analyze the cut quality. Attempts were made to draw conclusions on the influence of high beam quality on the cutting speed and cut quality. The cutting speeds were enormous for the disk and fiber laser cutting experiments with the 1.3mm and 2.3mm sheet thickness and the cut quality was good. The disk and fiber laser cutting speeds were lower at 4.3mm and 6.2mm sheet thickness but there was still a considerable percentage increase in cutting speeds compared to the CO2 laser cutting speeds at similar sheet thickness. However, the cut quality for 6.2mm thickness was not very good for the disk and fiber laser cutting experiments but could probably be improved by proper selection of cutting parameters.

Cutting of Frozen Wood

The objective of this master's thesis was to develop a system for measuring the cutting forces of frozen wood. In northern parts of the world cuttingof frozen wood is one of the major problem. During winter and early spring the temperature inside the wood cells will fall below Zero degrees that strongly influences on the properties of the wood. These variations of properties will effects on the blade nomenclature while cutting the frozen wood. However the end results will cause uneven cutting forces. Cutting forces, Chip formation, wearing of the blade and the quality of the machined surface are difficult task. In this project we are attempting to find the variation of cutting forces and properties of frozen wood at four different temperatures (-20 , -10, 0 and + 10 degrees). The linear planning machine was used for measuring the cuttingforces. The cutting was done parallel to the long axis of wood due to the nature of pine wood and the structure of the plane. A considerable amount of work andtime was used for collecting and processing the numerical information from the sensors of the measuring system. There were some alterations suggested to the construction of the plane and the sensor system.

Fiber Laser Cutting of Mild Steel

Fiber laser for materials processing have undergone a rapid development in the pastseveral years. As fiber laser provides a combination of high beam quality and awavelength that is easily absorbed by metal surfaces, the named future laser isexpected to challenge the CO2 and Nd:YAG lasers in the area of metal cutting. This thesis studied the performance of fiber laser cutting mild steel. In the literature review part, it introduced the laser cutting principle and the principle of fiber laser including the newest development of fiber laser cuttingtechnology. Because the fiber laser cutting mild steel is a very young technology, a preliminary test was made in order to investigate effect of the cutting parameters on cut quality. Then the formal fiber laser cutting experiment was madeby using 3 mm thickness S355 steel with oxygen as assistant gas. The experimentwas focused on the cut quality with maximum cutting speed and minimum oxygen gas pressure. And the cut quality is mainly decided by the kerf width, perpendicularity tolerance, surface roughness and striation patterns. After analysis the cutting result, several conclusions were made. Although the best result got in the experiment is not perfect as predicted, the whole result of the test can be accepted. Compared with CO2 laser, a higher cutting speed was achieved by fiber laser with very low oxygen gas pressure. A further improvement about the cutting quality might be possible by proper selection of process parameters. And in order to investigate the cutting performance more clearly, a future study about cutting different thickness mild steel and different shape was recommended.

Cutting edge: alum adjuvant stimulates inflammatory dendritic cells through activation of the NALP3 inflammasome.

Adjuvants are vaccine additives that stimulate the immune system without having any specific antigenic effect of itself. In this study we show that alum adjuvant induces the release of IL-1beta from macrophages and dendritic cells and that this is abrogated in cells lacking various NALP3 inflammasome components. The NALP3 inflammasome is also required in vivo for the innate immune response to OVA in alum. The early production of IL-1beta and the influx of inflammatory cells into the peritoneal cavity is strongly reduced in NALP3-deficient mice. The activation of adaptive cellular immunity to OVA-alum is initiated by monocytic dendritic cell precursors that induce the expansion of Ag-specific T cells in a NALP3-dependent way. We propose that, in addition to TLR stimulators, agonists of the NALP3 inflammasome should also be considered as vaccine adjuvants.

A mechanism of carbapenem resistance due to a new insertion element (ISPa133) in Pseudomonas aeruginosa

This study explored the evolutionary mechanism by which the clinical isolate PA110514 yields the imipenemresistant derivative PA116136. Both isolates were examined by PFGE and SDS-PAGE, which led to the identification of a new insertion sequence, ISPa133. This element was shown to have distinct chromosomal locations in each of the original isolates that appeared to explain the differences in imipenem susceptibilty. In strain PA110514, ISPa133 is located 56 nucleotides upstream of the translational start codon, which has no effect on expression of the porin OprD. However, in strain PA116136 ISPa133 it is located in front of nucleotide 696 and, by interrupting the coding region, causes a loss of OprD expression, thus conferring imipenem resistance. In vitro experiments mimicking the natural conditions of selective pressure yielded imipenem-resistant strains in which ISPa133 similarly interrupted oprD. A mechanism is proposed whereby ISPa133 acts as a mobile switch, with its position in oprD depending on the degree of selective pressure exerted by imipenem

A mechanism of carbapenem resistance due to a new insertion element (ISPa133) in Pseudomonas aeruginosa

This study explored the evolutionary mechanism by which the clinical isolate PA110514 yields the imipenemresistant derivative PA116136. Both isolates were examined by PFGE and SDS-PAGE, which led to the identification of a new insertion sequence, ISPa133. This element was shown to have distinct chromosomal locations in each of the original isolates that appeared to explain the differences in imipenem susceptibilty. In strain PA110514, ISPa133 is located 56 nucleotides upstream of the translational start codon, which has no effect on expression of the porin OprD. However, in strain PA116136 ISPa133 it is located in front of nucleotide 696 and, by interrupting the coding region, causes a loss of OprD expression, thus conferring imipenem resistance. In vitro experiments mimicking the natural conditions of selective pressure yielded imipenem-resistant strains in which ISPa133 similarly interrupted oprD. A mechanism is proposed whereby ISPa133 acts as a mobile switch, with its position in oprD depending on the degree of selective pressure exerted by imipenem