Length Change of P. C. Concrete Due to Moisture Content, MLR-85-09, 1987

Portland cement concrete is an outstanding structural material but stresses and cracks often occur in large structures due to drying shrinkage. The objective of this research was to determine the change in length due to loss of moisture from placement through complete drying of portland cement concrete. The drying shrinkage was determined for four different combinations of Iowa DOT structural concrete mix proportions and materials. The two mix proportions used were an Iowa DOT D57 (bridge deck mix proportions) and a water reduced modified C4 mix. Three 4"x 4"x 18" beams were made for each mix. After moist curing for three days, all beams were maintained in laboratory dry air and the length and weight were measured at 73°F ± 3°F. The temperature was cycled on alternate days from 73°F to 90°F through four months. From four months through six months, the temperature was cycled one day at 73°F and six days at 130°F. It took approximately six months for the concrete to reach a dry condition with these temperatures. The total drying shrinkage for the four mixes varied from .0106 in. to .0133 in. with an average of .0120 in. The rate of shrinkage was approximately .014% shrinkage per 1% moisture loss for all four mixes. The rate and total shrinkage for all four mixes was very similar and did not seem to depend on the type of coarse aggregate or the use of a retarder.

Active deformation fields: dense deformation field estimation for atlas-based segmentation using the active contour framework.

This paper presents a new and original variational framework for atlas-based segmentation. The proposed framework integrates both the active contour framework, and the dense deformation fields of optical flow framework. This framework is quite general and encompasses many of the state-of-the-art atlas-based segmentation methods. It also allows to perform the registration of atlas and target images based on only selected structures of interest. The versatility and potentiality of the proposed framework are demonstrated by presenting three diverse applications: In the first application, we show how the proposed framework can be used to simulate the growth of inconsistent structures like a tumor in an atlas. In the second application, we estimate the position of nonvisible brain structures based on the surrounding structures and validate the results by comparing with other methods. In the final application, we present the segmentation of lymph nodes in the Head and Neck CT images, and demonstrate how multiple registration forces can be used in this framework in an hierarchical manner.

Characterization of polyphosphate synthesis by isolated yeast vacuoles

Polyphosphate (iPOP) is a linear polymer of orthophosphate units linked together by high energy phosphoanhydride bonds. It is found in all organisms, localized in organelles called acidocalcisomes and ranges from a few to few hundred monomers in length. iPOP has been found to play a vast array of roles in all organisms, including phosphate and energy metabolism, regulation of enzymes, virulence, pathogenicity, bone remodelling and blood clotting, among many others. Recently it was found that iPOP levels were increased in myeloma cells. The growing interest in iPOP in human cell lines makes it an interesting molecule to study. However, not much is known about its metabolism in eukaryotes. Acidocalcisomes are electron dense, acidic organelles that belong to the group of Lysosome Related Organelles (LROs). The conservation of acidocalcisomes among all kingdoms of life is suggestive of their important roles for the organisms. However, they are difficult to analyse because of limited biochemical tools for investigation. Yeast vacuoles present remarkable similarities to acidocalcisomes in terms of their physiological and structural features, including synthesis and storage of iPOP, which make them an ideal candidate to study biological processes which are shared between vacuoles and acidocalcisomes. The availability of tools for genetic manipulation and isolation of vacuoles makes yeast a candidate of choice for the characterization of iPOP synthesis in eukaryotes. Our group has identified the Vacuolar Transporter Chaperone (VTC) complex as iPOP polymerase and identified the catalytic subunit (Vtc4). The goal of my study was to characterize the process of iPOP synthesis by isolated vacuoles and to reconstitute iPOP synthesis in liposomes. The first step was to develop a method for monitoring iPOP by isolated vacuoles over time and comparing it with previously known methods. Next, a detailed characterization was performed to determine the modulators of the process, both for intact as well as solubilized vacuoles. Finally, attempts were made to purify the VTC complex and reconstitute it in liposomes. A parallel line of study was the translocation and storage of synthesized iPOP in the lumen of the vacuoles. As a result of this study, it is possible to determine distinct pools of iPOP- inside and outside the vacuolar lumen. Additionally, I establish that the vacuolar lysate withstands harsh steps during reconstitution on liposomes and retains iPOP synthesizing activity. The next steps will be purification of the intact VTC complex and its structure determination by cryo-electron microscopy. - Les organismes vivants sont composés d'une ou plusieurs cellules responsables des processus biologiques élémentaires tels que la digestion, la respiration, la synthèse et la reproduction. Leur environnement interne est en équilibre et ils réalisent un très grand nombre de réactions chimiques et biochimiques pour maintenir cet équilibre. A différents compartiments cellulaires, ou organelles, sont attribuées des tâches spécifiques pour maintenir les cellules en vie. L'étude de ces fonctions permet une meilleure compréhension de la vie et des organismes vivants. De nombreux processus sont bien connus et caractérisés mais d'autres nécessitent encore des investigations détaillées. L'un de ces processus est le métabolisme des polyphosphates. Ces molécules sont des polymères linéaires de phosphate inorganique dont la taille peut varier de quelques dizaines à quelques centaines d'unités élémentaires. Ils sont présents dans tous les organismes, des bactéries à l'homme. Ils sont localisés principalement dans des compartiments cellulaires appelés acidocalcisomes, des organelles acides observés en microscopie électronique comme des structures denses aux électrons. Les polyphosphates jouent un rôle important dans le stockage et le métabolisme de l'énergie, la réponse au stress, la virulence, la pathogénicité et la résistance aux drogues. Chez l'homme, ils sont impliqués dans la coagulation du sang et le remodelage osseux. De nouvelles fonctions biologiques des polyphosphates sont encore découvertes, ce qui accroît l'intérêt des chercheurs pour ces molécules. Bien que des progrès considérables ont été réalisés afin de comprendre la fonction des polyphosphates chez les bactéries, ce qui concerne la synthèse, le stockage et la dégradation des polyphosphates chez les eucaryotes est mal connu. Les vacuoles de la levure Saccharomyces cerevisiae sont similaires aux acidocalcisomes des organismes supérieurs en termes de structure et de fonction. Les acidocalcisomes sont difficiles à étudier car il n'existe que peu d'outils génétiques et biochimiques qui permettent leur caractérisation. En revanche, les vacuoles peuvent être aisément isolées des cellules vivantes et manipulées génétiquement. Les vacuoles comme les acidocalcisomes synthétisent et stockent les polyphosphates. Ainsi, les découvertes faites grâce aux vacuoles de levures peuvent être extrapolées aux acidocalcisomes des organismes supérieurs. Le but de mon projet était de caractériser la synthèse des polyphosphates par des vacuoles isolées. Au cours de mon travail de thèse, j'ai mis au point une méthode de mesure de la synthèse des polyphosphates par des organelles purifés. Ensuite, j'ai identifié des composés qui modulent la réaction enzymatique lorsque celle-ci a lieu dans la vacuole ou après solubilisation de l'organelle. J'ai ainsi pu mettre en évidence deux groupes distincts de polyphosphates dans le système : ceux au-dehors de la vacuole et ceux en-dedans de l'organelle. Cette observation suggère donc très fortement que les vacuoles non seulement synthétisent les polyphosphates mais aussi transfère les molécules synthétisées de l'extérieur vers l'intérieur de l'organelle. Il est très vraisemblable que les vacuoles régulent le renouvellement des polyphosphates qu'elles conservent, en réponse à des signaux cellulaires. Des essais de purification de l'enzyme synthétisant les polyphosphates ainsi que sa reconstitution dans des liposomes ont également été entrepris. Ainsi, mon travail présente de nouveaux aspects de la synthèse des polyphosphates chez les eucaryotes et les résultats devraient encourager l'élucidation de mécanismes similaires chez les organismes supérieurs. - Les polyphosphates (iPOP) sont des polymères linéaires de phosphates inorganiques liés par des liaisons phosphoanhydres de haute énergie. Ces molécules sont présentes dans tous les organismes et localisées dans des compartiments cellulaires appelés acidocalcisomes. Elles varient en taille de quelques dizaines à quelques centaines d'unités phosphate. Des fonctions nombreuses et variées ont été attribuées aux iPOP dont un rôle dans les métabolismes de l'énergie et du phosphate, dans la régulation d'activités enzymatiques, la virulence, la pathogénicité, le remodelage osseux et la coagulation sanguine. Il a récemment été montré que les cellules de myélome contiennent une grande quantité de iPOP. Il y donc un intérêt croissant pour les iPOP dans les lignées cellulaires humaines. Cependant, très peu d'informations sur le métabolisme des iPOP chez les eucaryotes sont disponibles. Les acidocalcisomes sont des compartiments acides et denses aux électrons. Ils font partie du groupe des organelles similaires aux lysosomes (LROs pour Lysosome Related Organelles). Le fait que les acidocalcisomes soient conservés dans tous les règnes du vivant montrent l'importance de ces compartiments pour les organismes. Cependant, l'analyse de ces organelles est rendue difficile par l'existence d'un nombre limité d'outils biochimiques permettant leur caractérisation. Les vacuoles de levures possèdent des aspects structuraux et physiologiques très similaires à ceux des acidocalcisomes. Par exemple, ils synthétisent et gardent en réserve les iPOP. Ceci fait des vacuoles de levure un modèle idéal pour l'étude de processus biologiques conservés chez les vacuoles et les acidocalcisomes. De plus, la levure est un organisme de choix pour l'étude de la synthèse des iPOP compte-tenu de l'existence de nombreux outils génétiques et la possibilité d'isoler des vacuoles fonctionnelles. Notre groupe a identifié le complexe VTC (Vacuole transporter Chaperone) comme étant responsable de la synthèse des iPOP et la sous-unité Vtc4p comme celle possédant l'activité catalytique. L'objectif de cette étude était de caractériser le processus de synthèse des iPOP en utilisant des vacuoles isolées et de reconstituer la synthèse des iPOP dans des liposomes. La première étape a consisté en la mise au point d'un dosage permettant la mesure de la quantité de iPOP synthétisés par les organelles isolés en fonction du temps. Cette nouvelle méthode a été comparée aux méthodes décrites précédemment dans la littérature. Ensuite, la caractérisation détaillée du processus a permis d'identifier des composés modulateurs de la réaction à la fois pour des vacuoles intactes et des vacuoles solubilisées. Enfin, des essais de purification du complexe VTC et sa reconstitution dans des liposomes ont été entrepris. De façon parallèle, une étude sur la translocation et le stockage des iPOP dans le lumen des vacuoles a été menée. Il a ainsi été possible de mettre en évidence différents groupes de iPOP : les iPOP localisés à l'intérieur et ceux localisés à l'extérieur des vacuoles isolées. De plus, nous avons observé que le lysat vacuolaire n'est pas détérioré par les étapes de reconstitution dans les liposomes et conserve l'activité de synthèse des iPOP. Les prochaines étapes consisteront en la purification du complexe intact et de la détermination de sa structure par cryo-microscopie électronique.

Regulation of dendritic development by neurotrophic factors

AbstractEstablishment of a functional nervous system occurs through an orchestrated multistep process during embryogenesis. As dendrites are the primary sites of synaptic connections, development of dendritic arborization is essential for the formation of functional neural circuits. Maturation of dendritic arbor occurs through dynamic processes that are regulated by intrinsic genetic factors and external signals, such as environmental stimuli, neuronal activity and growth factors. Among the latter, the neurotrophic factor BDNF is a key regulator of dendritic growth. However, the mechanisms by which BDNF controls dendritic development remain elusive.In this study, we first showed that activation of the MAPK signaling pathway and phosphorylation of the transcription factor CREB are required to mediate the effects of BDNF on dendritic development of cortical neurons. However, phosphorylation of CREB alone is not sufficient to induce dendritic growth in response to BDNF. Thus, by using a mutant form of CREB unable to bind its coactivator CRTC1, we demonstrated that BDNF-induced dendritic elaboration requires the functional interaction between CREB and CRTC1. Consistent with these observations, inhibition of CRTC1 expression by shRNA-mediated knockdown was found to suppress the effects of BDNF on dendritic length and branching of cortical neurons.The nuclear translocation of CRTC1, a step necessary for the interaction between CREB and CRTC1, was shown to result from the activation of NMD A receptors by glutamate, leading to the dephosphorylation of CRTC1 by the protein phosphatase calcineurin. In line with these findings, prevention of CRTC1 nuclear translocation in the absence of glutamate, or by inhibiting NMDA receptors or calcineurin suppressed the promotion of dendritic growth by BDNF.Increasing evidence supports a role for the growth factor HGF in the regulation of dendritic morphology during brain development. Despite these observations, little is known about the cellular mechanisms underlying the effects of HGF on dendritic elaboration of cortical neurons. The second part of this study was aimed at elucidating the cellular processes that mediate the effects of HGF on dendritic differentiation. We found that HGF increases cortical dendritic growth through mechanisms that involve MAPK-dependent phosphorylation of CREB, and interaction of CREB with its coactivator CRTC1. These data indicate that the mechanisms underlying the promotion of dendritic growth by HGF are similar to those that mediate the effects of BDNF, suggesting that the role of CREB and CRTC1 in the regulation of dendritic development may not be limited to HGF and BDNF, but may extend to other neurotrophic factors that control dendritic differentiation.Together, these results identify a previously unrecognized mechanism by which CREB and its coactivator CRTC1 mediate the effects of BDNF and HGF on dendritic growth of cortical neurons. Moreover, these data highlight the important role of the cooperation between BDNF/HGF and glutamate that converges on CREB to stimulate the expression of genes that contribute to the development of dendritic arborization.RésuméL'établissement d'un système nerveux fonctionnel s'accomplit grâce à des mécanismes précis, orchestrés en plusieurs étapes au cours de l'embryogenèse. Les dendrites étant les principaux sites de connexions synaptiques, le développement de l'arborisation dendritique est essentiel à la formation de circuits neuronaux fonctionnels. La maturation de l'arbre dendritique s'effectue grâce à des processus dynamiques qui sont régulés par des facteurs génétiques intrinsèques ainsi que par des facteurs externes tels que les stimuli environnementaux, l'activité neuronale ou les facteurs de croissance. Parmi ces derniers, le facteur neurotrophique BDNF est - connu pour être un régulateur clé de la croissance dendritique. Cependant, les mécanismes par lesquels BDNF contrôle le développement dendritique demeurent mal connus.Au cours de cette étude, nous avons montré dans un premier temps que l'activation de la voie de signalisation de la MAPK et la phosphorylation du facteur de transcription CREB sont nécessaires aux effets du BDNF sur le développement dendritique des neurones corticaux. Toutefois, la phosphorylation de CREB en tant que telle n'est pas sûffisante pour permettre la pousse des dendrites en réponse au BDNF. Ainsi, en utilisant une forme mutée de CREB incapable de se lier à son coactivateur CRTC1, nous avons démontré que l'élaboration des dendrites induite par le BDNF nécessite également une interaction fonctionnelle entre CREB et CRTC1. Ces résultats ont été confirmés par d'autres expériences qui ont montré que l'inhibition de l'expression de CRTC1 par l'intermédiaire de shRNA supprime les effets du BDNF sur la longueur et le branchement dendritique des neurones corticaux.Les résultats obtenus au cours de ce travail montrent également que la translocation nucléaire de CRTC1, qui est une étape nécessaire à l'interaction entre CREB et CRTC1, résulte de l'activation des récepteurs NMDA par le glutamate, entraînant la déphosphorylation de CRTC1 par la protéine phosphatase calcineurine. De plus, le blocage de la translocation nucléaire de CRTC1 en absence de glutamate, ou suite à l'inhibition des récepteurs NMDA ou de la calcineurine, supprime complètement la pousse des dendrites induite par le BDNF.De nombreuses d'évidences indiquent que le facteur de croissance HGF joue également un rôle important dans la régulation de la morphologie dendritique au cours du développement cérébral. Malgré ces observations, peu d'éléments sont connus quant aux mécanismes cellulaires qui sous-tendent les effets du HGF sur la croissance dendritique des neurones corticaux. Le but de la seconde partie de cette étude a eu pour but d'élucider les processus cellulaires responsables des effets du HGF sur la différenciation dendritique des neurones corticaux. Au cours de ces expériences, nous avons pu mettre en évidence que le HGF induit la pousse dendritique par des mécanismes qui impliquent la phosphorylation de CREB par la MAPK, et l'interaction de CREB avec son coactivateur CRTC1. Ces données indiquent que les mécanismes impliqués dans la stimulation de la croissance dendritique par le HGF sont similaires à ceux régulant les effets du BDNF, ce qui suggère que le rôle de CREB et de CRTC1 dans la régulation du développement dendritique n'est vraisemblablement pas limité aux effets du HGF ou du BDNF, mais pourrait s'étendre à d'autres facteurs neurotrophiques qui contrôlent la différenciation dendritique.En conclusion, ces résultats ont permis l'identification d'un nouveau mécanisme par lequel CREB et son coactivateur CRTC1 transmettent les effets du BDNF et du HGF sur la croissance dendritique de neurones corticaux. Ces observations mettent également en évidence le rôle important joué par la coopération entre BDNF/HGF et le glutamate, dans l'activation de CREB ainsi que dans l'expression de gènes qui participent au développement de l'arborisation dendritique des neurones corticaux.

CAVIN-3 regulates circadian period length and PER:CRY protein abundance and interactions.

In mammals, transcriptional autorepression by Period (PER) and Cryptochrome (CRY) protein complexes is essential for the generation of circadian rhythms. We have identified CAVIN-3 as a new, cytoplasmic PER2-interacting protein influencing circadian clock properties. Thus, CAVIN-3 loss- and gain-of-function shortened and lengthened, respectively, the circadian period in fibroblasts and affected PER:CRY protein abundance and interaction. While depletion of protein kinase Cδ (PKCδ), a known partner of CAVIN-3, had little effect on circadian gene expression, CAVIN-3 required the PKCδ-binding site to exert its effect on period length. This suggests the involvement of yet uncharacterized protein kinases. Finally, CAVIN-3 activity in circadian gene expression was independent of caveolae.

Molecular investigation of lymph nodes in colon cancer patients using one-step nucleic acid amplification (OSNA): a new road to better staging?

BACKGROUND: A new diagnostic system, called one-step nucleic acid amplification (OSNA), has recently been designed to detect cytokeratin 19 mRNA as a surrogate for lymph node metastases. The objective of this prospective investigation was to compare the performance of OSNA with both standard hematoxylin and eosin (H&E) analysis and intensive histopathology in the detection of colon cancer lymph node metastases. METHODS: In total, 313 lymph nodes from 22 consecutive patients with stage I, II, and III colon cancer were assessed. Half of each lymph node was analyzed initially by H&E followed by an intensive histologic workup (5 levels of H&E and immunohistochemistry analyses, the gold standard for the assessment of sensitivity/specificity of OSNA), and the other half was analyzed using OSNA. RESULTS: OSNA was more sensitive in detecting small lymph node tumor infiltrates compared with H&E (11 results were OSNA positive/H&E negative). Compared with intensive histopathology, OSNA had 94.5% sensitivity, 97.6% specificity, and a concordance rate of 97.1%. OSNA resulted in an upstaging of 2 of 13 patients (15.3%) with lymph node-negative colon cancer after standard H&E examination. CONCLUSIONS: OSNA appeared to be a powerful and promising molecular tool for the detection of lymph node metastases in patients with colon cancer. OSNA had similar performance in the detection of lymph node metastases compared with intensive histopathologic investigations and appeared to be superior to standard histology with H&E. Most important, the authors concluded that OSNA may lead to a potential upstaging of >15% of patients with colon cancer.

One-step nucleic acid amplification (OSNA): a new road to better staging in colon cancer patients?

Introduction: Approximately one fifth of stage I and II colon cancer patients will suffer from recurrent disease. This is partly due to the presence of small nodal tumour infiltrates, which are undetected by standard histopathology using Haematoxylin & Eosin (H&E) staining on one slice and thus may not receive beneficial adjuvant therapy. A new diagnostic, semi-automatic system, called one-step nucleic acid amplification (OSNA), was recently designed for the detection of cytokeratin 19 (CK19) mRNA as a surrogate for lymph node metastases. The objective of the present investigation was to compare the performance of OSNA with both standard H&E as well as intensive histopathologic analyses in the detection of colon cancer lymph node micro- and macro-metastases.Methods: In this prospective study 313 lymph nodes from 22 consecutive stage I - III colon cancer patients were assessed. Half of each lymph node was analysed initially based on one slice of H&E followed by an intensive histologic work-up (5 levels of H&E and immuno-histochemistry staining for each slice), the other half was analysed using OSNA.Results: All OSNA results were available after less than 40 minutes. Fifty-one lymph nodes were positive and 246 lymph nodes negative with both OSNA and standard H&E. OSNA was more sensitive to detect small nodal tumor infiltrates compared to H&E (11 OSNA pos. /H&E neg.). Compared to intensive histopathologic analyses, OSNA had a sensitivity of 94.5% and a specificity of 97.6% to detect lymph node micro- and macro-metastases with a concordance rate of 97.1%. An upstaging due to OSNA was found in 2/13 (15.3%) initially node negative colon cancer patients.Conclusion: OSNA appears to be a powerful and promising molecular tool for the detection of lymph node macro- and micro-metastases in colon cancer patients. OSNA has a similar performance in the detection of micro- and macro-metastases compared to intensive histopathologic investigations and appears to be superior to standard histology with H&E. Since the use of OSNA allows the analysis of the whole lymph node, the problem of sampling bias and undetected tumor deposits due to uninvestigated material will be overcome in the future and OSNA may thus improve staging in colon cancer patients. It is hoped that this improved staging will lead to better patient selection for adjuvant therapy and consecutively improved local and distant control as well as better overall survival.

Grade and Cross Slope Estimation from LIDAR-based Surface Models, 2003

Many transportation agencies maintain grade as an attribute in roadway inventory databases; however, the information is often in an aggregated format. Cross slope is rarely included in large roadway inventories. Accurate methods available to collect grade and cross slope include global positioning systems, traditional surveying, and mobile mapping systems. However, most agencies do not have the resources to utilize these methods to collect grade and cross slope on a large scale. This report discusses the use of LIDAR to extract roadway grade and cross slope for large-scale inventories. Current data collection methods and their advantages and disadvantages are discussed. A pilot study to extract grade and cross slope from a LIDAR data set, including methodology, results, and conclusions, is presented. This report describes the regression methodology used to extract and evaluate the accuracy of grade and cross slope from three dimensional surfaces created from LIDAR data. The use of LIDAR data to extract grade and cross slope on tangent highway segments was evaluated and compared against grade and cross slope collected using an automatic level for 10 test segments along Iowa Highway 1. Grade and cross slope were measured from a surface model created from LIDAR data points collected for the study area. While grade could be estimated to within 1%, study results indicate that cross slope cannot practically be estimated using a LIDAR derived surface model.

Combining phospholipases and a liquid lipase for one-step biodiesel production using crude oils

Background Enzymatic biodiesel is becoming an increasingly popular topic in bioenergy literature because of its potential to overcome the problems posed by chemical processes. However, the high cost of the enzymatic process still remains the main drawback for its industrial application, mostly because of the high price of refined oils. Unfortunately, low cost substrates, such as crude soybean oil, often release a product that hardly accomplishes the final required biodiesel specifications and need an additional pretreatment for gums removal. In order to reduce costs and to make the enzymatic process more efficient, we developed an innovative system for enzymatic biodiesel production involving a combination of a lipase and two phospholipases. This allows performing the enzymatic degumming and transesterification in a single step, using crude soybean oil as feedstock, and converting part of the phospholipids into biodiesel. Since the two processes have never been studied together, an accurate analysis of the different reaction components and conditions was carried out. Results Crude soybean oil, used as low cost feedstock, is characterized by a high content of phospholipids (900 ppm of phosphorus). However, after the combined activity of different phospholipases and liquid lipase Callera Trans L, a complete transformation into fatty acid methyl esters (FAMEs >95%) and a good reduction of phosphorus (P <5 ppm) was achieved. The combination of enzymes allowed avoidance of the acid treatment required for gums removal, the consequent caustic neutralization, and the high temperature commonly used in degumming systems, making the overall process more eco-friendly and with higher yield. Once the conditions were established, the process was also tested with different vegetable oils with variable phosphorus contents. Conclusions Use of liquid lipase Callera Trans L in biodiesel production can provide numerous and sustainable benefits. Besides reducing the costs derived from enzyme immobilization, the lipase can be used in combination with other enzymes such as phospholipases for gums removal, thus allowing the use of much cheaper, non-refined oils. The possibility to perform degumming and transesterification in a single tank involves a great efficiency increase in the new era of enzymatic biodiesel production at industrial scale.

Estimation of forest canopy cover : a comparison of field measurement techniques

Abstract

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.