State of genomics and epigenomics research in the perspective of HIV cure.

PURPOSE OF REVIEW: One of the seven key scientific priorities identified in the road map on HIV cure research is to 'determine the host mechanisms that control HIV replication in the absence of therapy'. This review summarizes the recent work in genomics and in epigenetic control of viral replication that is relevant for this mission. RECENT FINDINGS: New technologies allow the joint analysis of host and viral transcripts. They identify the patterns of antisense transcription of the viral genome and its role in gene regulation. High-throughput studies facilitate the assessment of integration at the genome scale. Integration site, orientation and host genomic context modulate the transcription and should also be assessed at the level of single cells. The various models of latency in primary cells can be followed using dynamic study designs to acquire transcriptome and proteome data of the process of entry, maintenance and reactivation of latency. Dynamic studies can be applied to the study of transcription factors and chromatin modifications in latency and upon reactivation. SUMMARY: The convergence of primary cell models of latency, new high-throughput quantitative technologies applied to the study of time series and the identification of compounds that reactivate viral transcription bring unprecedented precision to the study of viral latency.

Nutritional and insulin regulation of fatty acid synthetase and leptin gene expression through ADD1/SREBP1.

The ability to regulate specific genes of energy metabolism in response to fasting and feeding is an important adaptation allowing survival of intermittent food supplies. However, little is known about transcription factors involved in such responses in higher organisms. We show here that gene expression in adipose tissue for adipocyte determination differentiation dependent factor (ADD) 1/sterol regulatory element binding protein (SREBP) 1, a basic-helix-loop-helix protein that has a dual DNA-binding specificity, is reduced dramatically upon fasting and elevated upon refeeding; this parallels closely the regulation of two adipose cell genes that are crucial in energy homeostasis, fatty acid synthetase (FAS) and leptin. This elevation of ADD1/SREBP1, leptin, and FAS that is induced by feeding in vivo is mimicked by exposure of cultured adipocytes to insulin, the classic hormone of the fed state. We also show that the promoters for both leptin and FAS are transactivated by ADD1/SREBP1. A mutation in the basic domain of ADD1/SREBP1 that allows E-box binding but destroys sterol regulatory element-1 binding prevents leptin gene transactivation but has no effect on the increase in FAS promoter function. Molecular dissection of the FAS promoter shows that most if not all of this action of ADD1/SREBP1 is through an E-box motif at -64 to -59, contained with a sequence identified previously as the major insulin response element of this gene. These results indicate that ADD1/SREBP1 is a key transcription factor linking changes in nutritional status and insulin levels to the expression of certain genes that regulate systemic energy metabolism.

Summary of Real Estate Assessment, 2009

The most important aspect of property taxation is the concept that all property should be valued for tax purposes on a uniform basis so that the actual property tax burden can be distributed equitably among individual property owners. One of the most widely used and accepted methods of determining relative levels and uniformity of assessments is the assessment/sales ratio study. Such a study, in its most fundamental analysis, is the comparison of the assessed value of an individual property to its sale price. For example, a property assessed at $12,000 which sold for $26,000 would have an assessment/sales ratio of 46% ($12,000 ÷ $26,000). The purpose of this study is to provide assessment/sales ratio information that may be utilized by property tax administrators, local assessing officials, and interested taxpayers in examining the relative levels and uniformity of assessments throughout the State of Iowa. After further refinement, the study is one factor considered by the Director of Revenue in the biennial equalization of assessments.

Summary of Real Estate Assessment, 2008

The most important aspect of property taxation is the concept that all property should be valued for tax purposes on a uniform basis so that the actual property tax burden can be distributed equitably among individual property owners. One of the most widely used and accepted methods of determining relative levels and uniformity of assessments is the assessment/sales ratio study. Such a study, in its most fundamental analysis, is the comparison of the assessed value of an individual property to its sale price. For example, a property assessed at $12,000 which sold for $26,000 would have an assessment/sales ratio of 46% ($12,000 ÷ $26,000). The purpose of this study is to provide assessment/sales ratio information that may be utilized by property tax administrators, local assessing officials, and interested taxpayers in examining the relative levels and uniformity of assessments throughout the State of Iowa. After further refinement, the study is one factor considered by the Director of Revenue in the biennial equalization of assessments.

Assessment of the soil compaction of two ultisols caused by logging operations

The impact of wood loads on bulk density and preconsolidation pressure and of harvester and forwarder traffic on rut depth, bulk density and preconsolidation pressure of two Ultisols were examined in this study. Our objective was to quantify the threshold beyond which significant soil compaction and rutting would occur. This study was carried out in the county of Eunápolis, state of Bahia, Brazil, (16 º 23 ' 17 '' S and 39 º 10 ' 06 '' W; altitude 80 m asl) in two Ultisols (PAd2 and PAd3) with different texture classes, in experimental areas with eucalypt plantation. The study involved measurements at the wood load site and machine driving at specific locations in the forest during logging operations. The treatments consisted of one harvester pass and, 8, 16 and 40 passes of a fully loaded forwarder. Thresholds were established based on the rut depth and percentage of preconsolidation pressure values in the region of additional soil compaction defined in the bearing capacity model. The percentage of soil samples with values of preconsolidation pressure in the region of additional soil compaction indicated a greater susceptibility of PAd3 than of PAd2 to soil compaction. The threshold levels established here based on preconsolidation pressure and rut depth indicated that no more than eight forwarder passes should be allowed in loading operations in order to minimize soil compaction.

Liming influence on soil chemical properties, nutritional status and yield of alfalfa grown in acid soil

Alfalfa is an important forage crop with high nutritive value, although highly susceptible to soil acidity. Liming is one of the most efficient and prevailing practices to correct soil acidity and improve alfalfa yield. The objective of this study was to evaluate response to liming of alfalfa grown in a greenhouse on a Typic Quartzipsamment soil. The treatments consisted of four lime rates (0, 3.8, 6.6 and 10.3 Mg ha-1) and two cuts. Alfalfa dry matter increased quadratically with increasing lime rates. In general, dry matter yield was maximized by a lime rate of 8.0 Mg ha-1. Except for the control, the dry matter nutrient contents in the treatments were adequate. The positive linear correlation between root and nodule dry matter with lime rates indicated improvement of these plant traits with decreasing soil acidity. The soil acidity indices pH, base saturation, Ca2+ concentration, Mg2+ concentration, and H + Al were relevant factors in the assessment of alfalfa yield. The magnitude of influence of these soil acidity indices on yield as determined by the coefficient of determination (R²) varied and decreased in the order: base saturation, H + Al, pH, Ca and Mg concentrations. Optimum values of selected soil chemical properties were defined for maximum shoot dry matter; these values can serve as a guideline for alfalfa liming to improve the yield of this forage on acid soils.

EGASP: the human ENCODE Genome Annotation Assessment Project.

BACKGROUND: We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. RESULTS: The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. CONCLUSION: This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.

Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

DRIS formulas for evaluation of nutritional status of cupuaçu trees

DRIS, an Diagnosis and Recommendation Integrated System, is a tool to evaluate the nutritional status of plants. Different DRIS formulas have been proposed to improve the efficiency of the crop nutrition diagnoses. The objective of this study was to compare the nutritional diagnosis of the formulas of Beaufils (1973), of Jones (1981) and of Elwali and Gascho (1984), based on the degree of agreement in commercial orchards of Theobrama grandiflorum trees. Leaf samples of 5 to 18 year-old cupuaçu trees were collected from 153 commercial orchards in agroforestry and monoculture systems in the state of Rondonia, Brazil. Bivariate relationships between nutrition concentrations in healthy trees were used to calculate DRIS norms. DRIS indices were calculated based on the different formulas and interpreted by the Potential Fertilizer Response method, in five categories. The DRIS norms, DRIS index calculations and their interpretations were developed using the DRIS Cupuaçu computer program (www.dris.com.br). The different DRIS formulas resulted in similar diagnoses with a degree of agreement of > 90% for the nutrients N, P, K, Ca, and Mg.

Assessment of micronutrient extractants from soils of Paraná, Brazil

In Brazil, plant-available micronutrients in the soil can be determined by several chemical extractants, the most common of which are dilute acid and chelating solutions. The purpose of this study was to assess the extractants 0.1 mol L-1 HCl, Mehlich-1, Mehlich-3 and DTPA for analysis of the micronutrients Cu, Zn, Fe, and Mn in soils from the state of Paraná. In samples from 12 soils (0-20 cm layer), wheat was planted (Triticum aestivum), grown for 42 days after emergence, and then bean (Phaseolus vulgaris) for 38 days. At the end of each planting period, the soil was sampled again. All extractants tested to assess the availability of Cu, Zn, Fe, and Mn correlated with each other. The efficiency of the extractants HCl, Mehlich-3 and DTPA in assessing plant-available Cu was similar, unlike Mehlich-1, which proved less efficient. The extractants HCl, Mehlich-1 and Mehlich-3 were less efficient in estimating plant-available Zn and Fe, and the most indicated extractant is DTPA. The efficiency of the extractants HCl, Mehlich-1, Mehlich-3 and DTPA in assessing plant-available Mn in soils from Paraná was similar.

State-of-the-art of 3D cultures (organs-on-a-chip) in safety testing and pathophysiology.

Integrated approaches using different in vitro methods in combination with bioinformatics can (i) increase the success rate and speed of drug development; (ii) improve the accuracy of toxicological risk assessment; and (iii) increase our understanding of disease. Three-dimensional (3D) cell culture models are important building blocks of this strategy which has emerged during the last years. The majority of these models are organotypic, i.e., they aim to reproduce major functions of an organ or organ system. This implies in many cases that more than one cell type forms the 3D structure, and often matrix elements play an important role. This review summarizes the state of the art concerning commonalities of the different models. For instance, the theory of mass transport/metabolite exchange in 3D systems and the special analytical requirements for test endpoints in organotypic cultures are discussed in detail. In the next part, 3D model systems for selected organs--liver, lung, skin, brain--are presented and characterized in dedicated chapters. Also, 3D approaches to the modeling of tumors are presented and discussed. All chapters give a historical background, illustrate the large variety of approaches, and highlight up- and downsides as well as specific requirements. Moreover, they refer to the application in disease modeling, drug discovery and safety assessment. Finally, consensus recommendations indicate a roadmap for the successful implementation of 3D models in routine screening. It is expected that the use of such models will accelerate progress by reducing error rates and wrong predictions from compound testing.

Assessment of Efficiency and Adequacy of Retention Terraces

Due to losses caused by water erosion, the development of techniques that increase the efficiency of soil conservation practices is fundamental. Terracing of agricultural lands is an important conservation practice. Bearing in mind that improperly built terraces may negatively affect the landscape, the purpose of this work was to evaluate the efficiency as well as the adequacy of retention terraces. Assessments were performed in four terraces implanted in different states, all located in the mideastern region of the state of Minas Gerais. The water storage efficiency of the terraces was determined by comparing the effective with the required storage capacity, as established in the project. Proposals were also made for the adequacy of the assessed terraces, based on the correction of the characteristics that jeopardized storage efficiency. The storage efficiency of three of the four assessed terraces was below the required levels (0.5-13 %). The main properties influencing storage capacity were: uniformity of ridge crest height, terrace end closure, and the cross section finishing. In two of the three low-efficiency terraces, the correction of these characteristics proved sufficient to raise the storage efficiency to nearly 100 %.

Variability of soil fertility properties in areas planted to sugarcane in the State of Goias, Brazil

Soil sampling should provide an accurate representation of a given area so that recommendations for amendments of soil acidity, fertilization and soil conservation may be drafted to increase yield and improve the use of inputs. The aim of this study was to evaluate the variability of soil fertility properties of Oxisols in areas planted to sugarcane in the State of Goias, Brazil. Two areas of approximately 8,100 m² each were selected, representing two fields of the Goiasa sugarcane mill in Goiatuba. The sugarcane crop had a row spacing of 1.5 m and subsamples were taken from 49 points in the row and 49 between the row with a Dutch auger at depths of 0.0-0.2 and 0.2-0.4 m, for a total of 196 subsamples for each area. The samples were individually subjected to chemical analyses of soil fertility (pH in CaCl2, potential acidity, organic matter, P, K, Ca and Mg) and particle size analysis. The number of subsamples required to compose a sample within the acceptable ranges of error of 5, 10, 20 and 40 % of each property were computed from the coefficients of variation and the Student t-value for 95 % confidence. The soil properties under analysis exhibited different variabilities: high (P and K), medium (potential acidity, Ca and Mg) and low (pH, organic matter and clay content). Most of the properties analyzed showed an error of less than 20 % for a group of 20 subsamples, except for P and K, which were capable of showing an error greater than 40 % around the mean. The extreme variability in phosphorus, particularly at the depth of 0.2-0.4 m, attributed to banded application of high rates of P fertilizers at planting, places limitations on assessment of its availability due to the high number of subsamples required for a composite sample.

Assessment of pedotransfer functions for estimating soil water retention curves for the amazon region

Knowledge of the soil water retention curve (SWRC) is essential for understanding and modeling hydraulic processes in the soil. However, direct determination of the SWRC is time consuming and costly. In addition, it requires a large number of samples, due to the high spatial and temporal variability of soil hydraulic properties. An alternative is the use of models, called pedotransfer functions (PTFs), which estimate the SWRC from easy-to-measure properties. The aim of this paper was to test the accuracy of 16 point or parametric PTFs reported in the literature on different soils from the south and southeast of the State of Pará, Brazil. The PTFs tested were proposed by Pidgeon (1972), Lal (1979), Aina & Periaswamy (1985), Arruda et al. (1987), Dijkerman (1988), Vereecken et al. (1989), Batjes (1996), van den Berg et al. (1997), Tomasella et al. (2000), Hodnett & Tomasella (2002), Oliveira et al. (2002), and Barros (2010). We used a database that includes soil texture (sand, silt, and clay), bulk density, soil organic carbon, soil pH, cation exchange capacity, and the SWRC. Most of the PTFs tested did not show good performance in estimating the SWRC. The parametric PTFs, however, performed better than the point PTFs in assessing the SWRC in the tested region. Among the parametric PTFs, those proposed by Tomasella et al. (2000) achieved the best accuracy in estimating the empirical parameters of the van Genuchten (1980) model, especially when tested in the top soil layer.