Monoclonal antibody screening of a phage-displayed random peptide library reveals mimotopes of chemokine receptor CCR5: Implications for the tertiary structure of the receptor and for an n-terminal binding site for HIV-1 gp120

The chemokine receptor CCR5 contains seven transmembrane-spanning domains. It binds chemokines and acts as co-receptor for macrophage (m)-tropic (or R5) strains of HIV-1. Monoclonal antibodies (mAb) to CCR5, 3A9 and 5C7, were used for biopanning a nonapeptide cysteine (C)-constrained phage-displayed random peptide library to ascertain contact residues and define tertiary structures of possible epitopes on CCR5. Reactivity of antibodies with phagotopes was established by enzyme-linked immunosorbent assay (ELISA). mAb 3A9 identified a phagotope C-HASIYDFGS-C (3A9/1), and 5C7 most frequently identified C-PHWLRDLRV-C (5C7/1). Corresponding peptides were synthesized. Phagotopes and synthetic peptides reacted in ELISA with corresponding antibodies and synthetic peptides inhibited antibody binding to the phagotopes. Reactivity by immunofluorescence of 3A9 with CCR5 was strongly inhibited by the corresponding peptide. Both mAb 3A9 and 5C7 reacted similarly with phagotopes and the corresponding peptide selected by the alternative mAb. The sequences of peptide inserts of phagotopes could be aligned as mimotopes of the sequence of CCR5. For phage 3A9/1, the motif SIYD aligned to residues at the N terminus and FG to residues on the first extracellular loop; for 5C7/1, residues at the N terminus, first extracellular loop, and possibly the third extracellular loop could be aligned and so would contribute to the mimotope. The synthetic peptides corresponding to the isolated phagotopes showed a CD4-dependent reactivity with gp120 of a primary, m-tropic HIV-1 isolate. Thus reactivity of antibodies raised to CCR5 against phage-displayed peptides defined mimotopes that reflect binding sites for these antibodies and reveal a part of the gp120 binding sites on CCR5.

COL1A1 C-propeptide cleavage site mutation causes high bone mass, bone fragility and jaw lesions: A new cause of gnathodiaphyseal dysplasia?

Gnathodiaphyseal dysplasia (GDD) is a rare autosomal dominant condition characterized by bone fragility, irregular bone mineral density (BMD) and fibro-osseous lesions in the skull and jaw. Mutations in Anoctamin-5 (ANO5) have been identified in some cases. We aimed to identify the causative mutation in a family with features of GDD but no mutation in ANO5, using whole exome capture and massive parallel sequencing (WES). WES of two affected individuals (a mother and son) and the mother's unaffected parents identified a mutation in the C-propeptide cleavage site of COL1A1. Similar mutations have been reported in individuals with osteogenesis imperfecta (OI) and paradoxically increased BMD. C-propeptide cleavage site mutations in COL1A1 may not only cause 'high bone mass OI', but also the clinical features of GDD, specifically irregular sclerotic BMD and fibro-osseous lesions in the skull and jaw. GDD patients negative for ANO5 mutations should be assessed for mutations in type I collagen C-propeptide cleavage sites.

TMIO-pyrimid hybrids are profluorescent, site-directed spin labels for nucleic acids

We report the synthesis of a new class of molecules which are hybrids of long-lived tetramethylisoindolinoxyl (TMIO) radicals and the pyrido[1,2-a]benzimidazole (PyrImid) scaffold. These compounds represent a new lead for noncovalently binding nucleic acid probes, as they interact with nucleic acids with previously unreported C (DNA) and C/U (RNA) complementarity, which can be detected by electron paramagnetic resonance (EPR) techniques. They also have promising properties for fluorimetric analysis, as their fluorescent spin-quenched derivatives exhibit a significant Stokes shift

Probabilistic assessment of herbicide runoff from Japanese rice paddies: The effects of local meteorological conditions and site-specific water management

Uncertainty assessments of herbicide losses from rice paddies in Japan associated with local meteorological conditions and water management practices were performed using a pesticide fate and transport model, PCPF-1, under the Monte Carlo (MC) simulation scheme. First, MC simulations were conducted for five different cities with a prescribed water management scenario and a 10-year meteorological dataset of each city. The effectiveness of water management was observed regarding the reduction of pesticide runoff. However, a greater potential of pesticide runoff remained in Western Japan. Secondly, an extended analysis was attempted to evaluate the effects of local water management and meteorological conditions between the Chikugo River basin and the Sakura River basin using uncertainty inputs processed from observed water management data. The results showed that because of more severe rainfall events, significant pesticide runoff occurred in the Chikugo River basin even when appropriate irrigation practices were implemented. © Pesticide Science Society of Japan.

Site and gender specificity of inheritance of bone mineral density

Differences in genetic control of BMD by skeletal sites and genders were examined by complex segregation analysis in 816 members of 147 families with probands with extreme low BMD. Spine BMD correlated more strongly in male-male comparisons and hip BMD in female-female comparisons, consistent with gender- and site-specificity of BMD heritability. Introduction: Evidence from studies in animals and humans suggests that the genetic control of bone mineral density (BMD) may differ at different skeletal sites and between genders. This question has important implications for the design and interpretation of genetic studies of osteoporosis. Methods: We examined the genetic profile of 147 families with 816 individuals recruited through probands with extreme low BMD (T-score < −2.5, Z-score < −2.0). Complex segregation analysis was performed using the Pedigree Analysis Package. BMD was measured by DXA at both lumbar spine (L1-L4) and femoral neck. Results: Complex segregation analysis excluded purely monogenic and environmental models of segregation of lumbar spine and femoral neck BMD in these families. Pure polygenic models were excluded at the lumbar spine when menopausal status was considered as a covariate, but not at the femoral neck. Mendelian models with a residual polygenic component were not excluded. These models were consistent with the presence of a rare Mendelian genotype of prevalence 3–19 %, causing high BMD at the hip and spine in these families, with additional polygenic effects. Total heritability range at the lumbar spine was 61–67 % and at the femoral neck was 44–67 %. Significant differences in correlation of femoral neck and lumbar spine BMD were observed between male and female relative pairs, with male-male comparisons exhibiting stronger lumbar spine BMD correlation than femoral neck, and female-female comparisons having greater femoral neck BMD correlation than lumbar spine. These findings remained true for parent-offspring correlations when menopausal status was taken into account. The recurrence risk ratio for siblings of probands of a Z-score < −2.0 was 5.4 at the lumbar spine and 5.9 at the femoral neck. Conclusions: These findings support gender- and site-specificity of the inheritance of BMD. These results should be considered in the design and interpretation of genetic studies of osteoporosis.

The nature of the charge-ordered state in Y0.5Ca0.5MnO3 with a very small average radius of the A-site cations

A detailed investigation of Y0.5Ca0.5MnO3 with a very small radius of the A-site cations ([r(A)] approximate to 1.13 Angstrom reveals the occurrence of a charge-ordering transition in the paramagnetic state, at a relatively high temperature of 260 K. The orthorhombic lattice distortion, as measured by the dimensionless index D, is large (similar to 1.75%) over the entire 300-100 K range, but the antiferromagnetic interactions become prominent only at low temperatures (< 160 K). The charge-ordering gap in Y0.5Ca0.5MnO3, measured by low-temperature vacuum tunnelling spectroscopy, is large (similar to 0.5 eV) and the charge-ordered state is unaffected by the application of a magnetic field of 6 T. The study indicates that the nature of charge-ordering in Y0.5Ca0.5MnO3 which is dominated by the cooperative Jahn-Teller effect and the associated lattice distortion is distinctly different from analogous manganates with larger [r(A)].

The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have attracted attention. There are several limitations to experimentally testing such hypotheses, Recent developments in computational methods facilitate the study of active site-ligand complexes to high levels of accuracy, Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

Site-controlled growth of Ge nanostructures on Si(100) via pulsed laser deposition nanostenciling

The authors combine nanostenciling and pulsed laser deposition to patterngermanium(Ge)nanostructures into desired architectures. They have analyzed the evolution of the Ge morphology with coverage. Following the formation of a wetting layer within each area defined by the stencil’s apertures, Gegrowth becomes three dimensional and the size and number of Ge nanocrystals evolve with coverage. Micro-Raman spectroscopy shows that the deposits are crystalline and epitaxial. This approach is promising for the parallel patterning of semiconductor nanostructures for optoelectronic applications.

Artificial Neural Network Based Automatic Emergency Landing Site Selection for UAVs and Highly Automated Aircraft

In this report an artificial neural network (ANN) based automated emergency landing site selection system for unmanned aerial vehicle (UAV) and general aviation (GA) is described. The system aims increase safety of UAV operation by emulating pilot decision making in emergency landing scenarios using an ANN to select a safe landing site from available candidates. The strength of an ANN to model complex input relationships makes it a perfect system to handle the multicriteria decision making (MCDM) process of emergency landing site selection. The ANN operates by identifying the more favorable of two landing sites when provided with an input vector derived from both landing site's parameters, the aircraft's current state and wind measurements. The system consists of a feed forward ANN, a pre-processor class which produces ANN input vectors and a class in charge of creating a ranking of landing site candidates using the ANN. The system was successfully implemented in C++ using the FANN C++ library and ROS. Results obtained from ANN training and simulations using randomly generated landing sites by a site detection simulator data verify the feasibility of an ANN based automated emergency landing site selection system.

Death in the Bolivian High Plateau : Burials and Tiwanaku Society

My Ph.D. dissertation presents a multi-disciplinary analysis of the mortuary practices of the Tiwanaku culture of the Bolivian high plateau, situated at an altitude of c. 3800 m above sea level. The Tiwanaku State (c. AD 500-1150) was one of the most important pre-Inca civilisations of the South Central Andes. The book begins with a brief introductory chapter. In chapter 2 I discuss methodological and theoretical developments in archaeological mortuary studies from the late 1960s until the turn of the millennium. I am especially interested in the issue how archaeological burial data can be used to draw inferences on the social structure of prehistoric societies. Chapter 3 deals with the early historic sources written in the 16th and 17th centuries, following the Spanish Conquest of the Incas. In particular, I review information on how the Incas manifested status differences between and within social classes and what kinds of burial treatments they applied. In chapter 4 I compare the Inca case with 20th century ethnographic data on the Aymara Indians of the Bolivian high plateau. Even if Christianity has affected virtually every level of Aymara religion, surprisingly many traditional features can still be observed in present day Aymara mortuary ceremonies. The archaeological part of my book begins with chapter 5, which is an introduction into Tiwanaku archaeology. In the next chapter, I present an overview of previously reported Tiwanaku cemeteries and burials. Chapter 7 deals with my own excavations at the Late Tiwanaku/early post-Tiwanaku cemetery site of Tiraska, located on the south-eastern shore of Lake Titicaca. During the 1998, 2002, and 2003 field seasons, a total of 32 burials were investigated at Tiraska. The great majority of these were subterranean stone-lined tombs, each containing the skeletal remains of 1 individual and 1-2 ceramic vessels. Nine burials have been radiocarbon dated, the dates in question indicating that the cemetery was in use from the 10th until the 13th century AD. In chapter 8 I point out that considerable regional and/or ethnic differences can be noted between studied Tiwanaku cemetery sites. Because of the mentioned differences, and a general lack of securely dated burial contexts, I feel that at present we can do no better than to classify most studied Tiwanaku burials into three broad categories: (1) elite and/or priests, (2) "commoners", and (3) sacrificial victims and/or slaves and/or prisoners of war. On the basis of such indicators as monumental architecture and occupational specialisation we would expect to find considerable status-related differences in tomb size, grave goods, etc. among the Tiwanaku. Interestingly, however, such variation is rather modest, and the Tiwanaku seem to have been a lot less interested in expending considerable labour and resources in burial facilities than their pre-Columbian contemporaries of many parts of the Central Andes.

A Touch of Red : Archaeological and Ethnographic Approaches to Interpreting Finnish Rock Paintings

Approximately 125 prehistoric rock paintings have been found in the modern territory of Finland. The paintings were done with red ochre and are almost without exception located on steep lakeshore cliffs associated with ancient water routes. Most of the sites are found in the central and eastern parts of the country, especially on the shores of Lakes Päijänne and Saimaa. Using shore displacement chronology, the art has been dated to ca. 5000 – 1500 BC. It was thus created mainly during the Stone Age and can be associated with the so-called ‘Comb Ware’ cultures of the Subneolithic period. The range of motifs is rather limited, consisting mainly of schematic depictions of stick-figure humans, elks, boats, handprints and geometric signs. Few paintings include any evidence of narrative scenes, making their interpretation a rather difficult task. In Finnish archaeological literature, the paintings have traditionally been associated with ’sympathetic’ hunting magic, or the belief that the ritual shooting of the painted animals would increase hunting luck. Some writers have also suggested totemistic and shamanistic readings of the art. This dissertation is a critical review of the interpretations offered of Finnish rock art and an exploration of the potentials of archaeological and ethnographic research in increasing our knowledge of its meaning. Methods used include ’formal’ approaches such as archaeological excavation, landscape analysis and the application of neuropsychological research to the study of rock art, as well as ethnographically ’informed’ approaches that make use of Saami and Baltic Finnish ethnohistorical sources in interpretation. In conclusion, it is argued that although North European hunter-gatherer rock art is often thought to lie beyond the reach of ‘informed’ knowledge, the exceptional continuity of prehistoric settlement in Finland validates the informed approach in the interpretation of Finnish rock paintings. The art can be confidently associated with shamanism of the kind still practiced by the Saami of Northern Fennoscandia in the historical period. Evidence of similar shamanistic practices, concepts and cosmology are also found in traditional Finnish-Karelian epic poetry. Previous readings of the art based on ‘hunting magic’ and totemism are rejected. Most of the paintings appear to depict experiences of falling into a trance, of shamanic metamorphosis and trance journeys, and of ‘spirit helper’ beings comparable to those employed by the Saami shaman (noaidi). As demonstrated by the results of an excavation at the rock painting of Valkeisaari, the painted cliffs themselves find a close parallel in the Saami cult of the 'sieidi', or sacred cliffs and boulders worshipped as expressing a supernatural power. Like the Saami, the prehistoric inhabitants of the Finnish Lake Region seem to have believed that certain cliffs were ’alive’ and inhabited by the spirit helpers of the shaman. The rock paintings can thus be associated with shamanic vision quests, and the making of ‘art’ with an effort to socialize the other members of the community, especially the ritual specialists, with trance visions. However, the paintings were not merely to be looked at. The red ochre handprints pressed on images of elks, as well as the fact that many paintings appear ’smeared’, indicate that they were also to be touched – perhaps in order to tap into the supernatural potency inherent in the cliff and in the paintings of spirit animals.

Locus Bonus : The Relationship of the Roman Villa to its Environment in the Vicinity of Rome

The aim of this study is to examine the relationship of the Roman villa to its environment. The villa was an important feature of the countryside intended both for agricultural production and for leisure. Manuals of Roman agriculture give instructions on how to select a location for an estate. The ideal location was a moderate slope facing east or south in a healthy area and good neighborhood, near good water resources and fertile soils. A road or a navigable river or the sea was needed for transportation of produce. A market for selling the produce, a town or a village, should have been nearby. The research area is the surroundings of the city of Rome, a key area for the development of the villa. The materials used consist of archaeological settlement sites, literary and epigraphical evidence as well as environmental data. The sites include all settlement sites from the 7th century BC to 5th century AD to examine changes in the tradition of site selection. Geographical Information Systems were used to analyze the data. Six aspects of location were examined: geology, soils, water resources, terrain, visibility/viewability and relationship to roads and habitation centers. Geology was important for finding building materials and the large villas from the 2nd century BC onwards are close to sources of building stones. Fertile soils were sought even in the period of the densest settlement. The area is rich in water, both rainfall and groundwater, and finding a water supply was fairly easy. A certain kind of terrain was sought over very long periods: a small spur or ridge shoulder facing preferably south with an open area in front of the site. The most popular villa resorts are located on the slopes visible from almost the entire Roman region. A visible villa served the social and political aspirations of the owner, whereas being in the villa created a sense of privacy. The area has a very dense road network ensuring good connectivity from almost anywhere in the region. The best visibility/viewability, dense settlement and most burials by roads coincide, creating a good neighborhood. The locations featuring the most qualities cover nearly a quarter of the area and more than half of the settlement sites are located in them. The ideal location was based on centuries of practical experience and rationalized by the literary tradition.

Archaeology of wings : Birds and people in the Baltic Sea region during the Stone Age

The prominent roles of birds, often mentioned in historical sources, are not well reflected in archaeological research. Absence or scarcity of bird bones in archaeological assemblages has been often seen as indication of a minor role of birds in the prehistoric economy or ideology, or explained by taphonomic loss. Few studies exist where birds form the basis for extensive archaeological interpretation. In this doctoral dissertation bird bone material from various Stone Age sites in the Baltic Sea region is investigated. The study period is approximately 7000-3400 BP, comprising mainly Neolithic cultures. The settlement material comes from Finland, Åland, Gotland, Saaremaa and Hiiumaa. Osteological materials are used for studying the economic and cultural importance of birds, fowling methods and principal fowling seasons. The bones were identified and earlier identifications partially checked with help of a reference material of modern skeletons. Fracture analysis was used in order to study the deposition history of bones at Ajvide settlement site. Birds in burials at two large cemeteries, Ajvide on Gotland and Zvejnieki in northern Latvia were investigated in order to study the roles of birds in burial practices. My study reveals that the economic importance of birds is at least seasonally often more prominent than usually thought, and varies greatly in different areas. Fowling has been most important in coastal areas, and especially during the breeding season. Waterbirds and grouse species were generally the most important groups in Finnish Stone Age economy. The identified species composition shows much resemblance to contemporary hunting with species such as the mallard and capercaillie commonly found. Burial materials and additional archaeological evidence from Gotland, Latvia and some other parts of northern Europe indicate that birds –e.g., jay, whooper swan, ducks – have been socially and ideologically important for the studied groups (indicating a place in the belief system, e.g. clan totemism). The burial finds indicate that some common ideas about waterbirds (perhaps as messengers or spirit helpers) might have existed in the northern European Stone Age.

Competing A-site and B-site driven ferroelectric instabilities in the (1-x)PbTiO3-(x)BiAlO3 system

The system (1-x)PbTiO3-(x)BiAlO3 has been investigated with regard to its solid solubility, crystal structure, microstructure, and ferroelectric transition. The unit cell volume and the tetragonality exhibit anomalous behavior near x=0.10. The Curie point (T-C) of PbTiO3 was however found to be nearly unchanged. The study seems to suggest that the decrease in the stability of the ferroelectric state due to dilution of the Ti-sublattice by smaller sized Al+3 ions is compensated by the increase in the ferroelectric stability by the Bi+3 ions.

The Walls of Agios Donatos Zervochoriou : A case study of a fortress in Thesprotia, northwestern Greece

The study deals with the dating and the function of the fortress of Agios Donatos, which is located in the Kokytos river valley in Thesprotia, northwestern Greece. To solve the dating problem one had to use parallels found in research literature, preferably within as close range as possible. As most of the fortresses within a close proximity had not been adequately published, one had to use parallels within a larger area, throughout the Hellenistic world. Archaeological material found in trial trenches on site was used when possible. To think of the function of the site one had to study the site itself and its relation to the environment, and to compare the situation with the parallels found in research literature, mostly different archaeological survey projects in Greece and Asia Minor. The fortress was built during a period ranging from the final decades of the fourth century down to the mid-third century BC. Most likely it was built during the first quarter of the third century, that is the reign of Pyrrhus of Epirus when the area experienced a boom in fortress building activity. The function of the site was most likely to protect a trade route from the major port in the area to the central areas of the valley and on to Kalamas river, which was the major route on to Macedon. In the end an appendix dealing with the other fortified sites in Thesprotia has been compiled.