The ChIP-seq-defined networks of Bcl-3 gene binding support its required role in skeletal muscle atrophy

NF-kappaB transcriptional activation is required for skeletal muscle disuse atrophy. We are continuing to study how the activation of NF-kB regulates the genes that encode the protein products that cause atrophy. Using ChIP-sequencing we found that Bcl-3, an NF-kB transcriptional activator required for atrophy, binds to the promoters of a number of genes whose collective function describes two major aspects of muscle wasting. By means of bioinformatics analysis of ChIP-sequencing data we found Bcl-3 to be directing transcription networks of proteolysis and energy metabolism. The proteolytic arm of the Bcl-3 networks includes many E3 ligases associated with proteasomal protein degradation, including that of the N-end rule pathway. The metabolic arm appears to be involved in organizing the change from oxidative phosphorylation to glycolysis in atrophying muscle. For one gene, MuRF1, ChIP-sequencing data identified the location of Bcl-3 and p50 binding in the promoter region which directed the creation of deletant and base-substitution mutations of MuRF1 promoter constructs to determine the effect on gene transcription. The results provide the first direct confirmation that the NF-kB binding site is involved in the muscle unloading regulation of MuRF1. Finally, we have combined the ChIP-sequencing results with gene expression microarray data from unloaded muscle to map several direct targets of Bcl-3 that are transcription factors whose own targets describe a set of indirect targets for NF-kB in atrophy. ChIP-sequencing provides the first molecular explanation for the finding that Bcl3 knockout mice are resistant to disuse muscle atrophy. Mapping the transcriptional regulation of muscle atrophy requires an unbiased analysis of the whole genome, which we show is now possible with ChIP-sequencing.R01 AR041705 - NIAMS NIH HHS; R01 AR060217 - NIAMS NIH HHS; AR041705 - NIAMS NIH HHS; AR060217 - NIAMS NIH HH

Uncovering the sources of DNA found on the Turin Shroud

The Turin Shroud is traditionally considered to be the burial cloth in which the body of Jesus Christ was wrapped after his death approximately 2000 years ago. Here, we report the main findings from the analysis of genomic DNA extracted from dust particles vacuumed from parts of the body image and the lateral edge used for radiocarbon dating. Several plant taxa native to the Mediterranean area were identified as well as species with a primary center of origin in Asia, the Middle East or the Americas but introduced in a historical interval later than the Medieval period. Regarding human mitogenome lineages, our analyses detected sequences from multiple subjects of different ethnic origins, which clustered into a number of Western Eurasian haplogroups, including some known to be typical of Western Europe, the Near East, the Arabian Peninsula and the Indian sub-continent. Such diversity does not exclude a Medieval origin in Europe but it would be also compatible with the historic path followed by the Turin Shroud during its presumed journey from the Near East. Furthermore, the results raise the possibility of an Indian manufacture of the linen cloth

Systematizing Genome Privacy Research: A Privacy-Enhancing Technologies Perspective

Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare. However, this also prompts a number of security and privacy concerns stemming from the distinctive characteristics of genomic data. To address them, a new research community has emerged and produced a large number of publications and initiatives. In this paper, we rely on a structured methodology to contextualize and provide a critical analysis of the current knowledge on privacy-enhancing technologies used for testing, storing, and sharing genomic data, using a representative sample of the work published in the past decade. We identify and discuss limitations, technical challenges, and issues faced by the community, focusing in particular on those that are inherently tied to the nature of the problem and are harder for the community alone to address. Finally, we report on the importance and difficulty of the identified challenges based on an online survey of genome data privacy expertsComment: To appear in the Proceedings on Privacy Enhancing Technologies (PoPETs), Vol. 2019, Issue

MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution

BACKGROUND: MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. RESULTS: We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. CONCLUSION: MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at and

Virologic survey in stranded cetaceans from northern Portugal : insights on Cetacean poxvirus and Cetacean coronavirus

Dissertação de Mestrado Integrado em Medicina Veterinária, área científica de Sanidade AnimalWith an extended coastline, Portuguese waters harbor different resident and migratory species. It also registers a substantial amount of strandings every year (approximately 236 per year), which, under the supervision of ICNF, enabled the creation of a Marine Animal Tissue Bank, where tissue samples are stored for posterior analysis. Cetacean poxvirus is responsible for poxvirus skin disease, (pinhole or ring-like lesions) and tattoo skin disease. Phylogenetically 6 species are now identified (CePV1-6). Although this virus is not connected with high mortality rates, it may be lethal to neonates and calves without maternal immunity, severely impairing small isolated populations. To evaluate Poxvirus genetic diversity in skin lesions macroscopically compatible with Poxvirus, 47 samples collected between 2011 and 2015, from 4 different species of dolphins (Delphinus delphis, Tursiops truncates, Phocoena phocoena and Stenella coeruleoalba) were analyzed using a conventional PCR with a set of degenerate primers, previously designed for cetacean poxvirus screening. The positive samples (n=28, 58.33%) were further tested for the DNA polymerase gene, yielding 19 (40.4%) positive samples. After direct sequencing, a phylogenetic tree was designed based on the amino acidic sequences allowing the discrimination of 3 genetic clusters, genetically closer with CePV-1, CePV-5, CePV-3 and CePV-6. An unassigned cluster was also identified, suggesting the presence of a seventh subgroup (CePV-7). Contrary to cetacean poxvirus, Cetacean coronavirus was recently identified and included in the Gammacoronavirus genera. Since its discovery in 2008, cetacean coronavirus was detected in Hong Kong and United States in captives or semi-captive bottlenose dolphins presenting anorexia, diarrhea and lethargy. The movement, dispersion, and incidence of this virus in the wild is still unknown. It is important to highlight the taxonomic assignment of this virus in the Gammacoronavirus genera, which previously included coronavirus affecting strictly birds. A total of fifty-five (n=55) samples were analyzed, collected from 5 cetacean species (Delphinus delphis, Tursiops truncates, Phocoena phocoena, Stenella coeruleoalba and Kogia breviceps), between 2012-2021. The viral screening was performed with a pancoronavirus rt-PCR assay, due to the unavailability of a specific tool. However, no positive samples were detected. The distribution, evolution and prevalence of this vírus remains unknownRESUMO - Rastreio virológico em cetáceos arrojados do norte de Portugal : considerações sobre poxvírus e o coronavírus cetáceo - Com uma costa marítima extensa, as águas portuguesas albergam diferentes espécies animais, residentes e migratórias. Registam também um elevado número de arrojamentos anuais (aproximadamente 236 anuais), permitindo a recolha padronizada de amostras biológicas e a criação de um Banco de Tecidos pela Rede de Arrojamentos e ICNF. O Poxvírus dos cetáceos é responsável pelo aparecimento de lesões cutâneas muito características e já amplamente estudadas (lesões pinhole ou em forma de anel) e pela tattoo skin disease (TSD). Presentemente são reconhecidos 6 grupos filogenéticos distintos (CePV1-6). Embora este vírus não esteja relacionado com altas taxas de mortalidade, pode ser responsável pela mortalidade de neonatos e juvenis sem imunidade materna e de pequenas populações isoladas. Um total de 47 amostras de lesões de pele, colhidos entre os anos de 2011 e 2015, e pertencentes a 4 espécies diferentes de golfinhos (Delphinus delphis, Tursiops truncates, Phocoena phocoena e Stenella coeruleoalba), foram analisadas por PCR convencional, utilizando um conjunto de oligonucleotideos degenerados. As amostras positivas (n=28, 58,33%) foram posteriormente testadas para o gene da DNA polimerase, onde 19 (40,4%) testaram positivo. Os produtos foram posteriormente sequenciados, e as sequências amino acídicas utilizadas na construção de uma árvore filogenética. As sequências dos poxvírus nacionais mostraram-se geneticamente mais próximos dos grupos CePV-1, 5, 3 e 6. Foi também identificado um novo agrupamento das amostras sequenciadas, sugerindo a existência de um sétimo grupo (CePV-7). Contrariamente ao Poxvirus, o coronavírus cetáceo foi apenas recentemente identificado e incluído no género Gammacoronavirus. Desde a sua identificação numa baleia beluga em 2008, este vírus foi detetado anos mais tarde em Hong Kong e nos Estados Unidos, em golfinhos-roazes em regime de cativeiro ou semicativeiro, com variadas apresentações clínicas. Um total de cinquenta e cinco (n=55) amostras foram analisadas recorrendo a rt-PCR, incluindo amostras de 5 espécies de cetáceos (Delphinus delphis, Tursiops truncates, Phocoena phocoena, Stenella coeruleoalba e Kogia breviceps). As amostras correspondiam a arrojamentos ocorridos entre os anos de 2012 a 2021, não tendo sido detetadas quaisquer amostras positivas. O movimento, dispersão e prevalência deste vírus na natureza permanece desconhecidoN/

PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories

<p>Abstract</p> <p>Background</p> <p>Most molecular biology experiments, and the techniques associated with this field of study, involve a great deal of engineering in the form of molecular cloning. Like all forms of engineering, perfect information about the starting material is crucial for successful completion of design and strategies.</p> <p>Results</p> <p>We have generated a program that allows complete <it>in silico </it>simulation of the cloning experiment. Starting with a primary DNA sequence, PlasmaDNA looks for restriction sites, open reading frames, primer annealing sequences, and various common domains. The databases are easily expandable by the user to fit his most common cloning needs. PlasmaDNA can manage and graphically represent multiple sequences at the same time, and keeps in memory the overhangs at the end of the sequences if any. This means that it is possible to virtually digest fragments, to add the digestion products to the project, and to ligate together fragments with compatible ends to generate the new sequences. Polymerase Chain Reaction (PCR) fragments can also be virtually generated using the primer database, automatically adding to the fragments any 5' extra sequences present in the primers.</p> <p>Conclusion</p> <p>PlasmaDNA is a program available both on Windows and Apple operating systems, designed to facilitate molecular cloning experiments by building a visual map of the DNA. It then allows the complete planning and simulation of the cloning experiment. It also automatically updates the new sequences generated in the process, which is an important help in practice. The capacity to maintain multiple sequences in the same file can also be used to archive the various steps and strategies involved in the cloning of each construct. The program is freely available for download without charge or restriction.</p

Tangible user interfaces : past, present and future directions

In the last two decades, Tangible User Interfaces (TUIs) have emerged as a new interface type that interlinks the digital and physical worlds. Drawing upon users' knowledge and skills of interaction with the real non-digital world, TUIs show a potential to enhance the way in which people interact with and leverage digital information. However, TUI research is still in its infancy and extensive research is required in or- der to fully understand the implications of tangible user interfaces, to develop technologies that further bridge the digital and the physical, and to guide TUI design with empirical knowledge. This paper examines the existing body of work on Tangible User In- terfaces. We start by sketching the history of tangible user interfaces, examining the intellectual origins of this field. We then present TUIs in a broader context, survey application domains, and review frame- works and taxonomies. We also discuss conceptual foundations of TUIs including perspectives from cognitive sciences, phycology, and philoso- phy. Methods and technologies for designing, building, and evaluating TUIs are also addressed. Finally, we discuss the strengths and limita- tions of TUIs and chart directions for future research

Microbial Biodegradation of Lignocellulose for Ethanol Production

Bioethanol can be produced from a range of substrates and it is considered to be renewable. Lignocellulose is one of the substrates that can be used for bioethanol production. Genetic engineering of a microorganism that can completely convert all the sugars of cellulosic material into ethanol is one of the important steps for the production process. This study has two parts that aim to produce bioethanol by using genetically modified microorganisms. The first part of the study deals with bioethanol production from lignocellulosic material by microbial fermentation in two steps. The first step is the degradation of the lignocellulosic material by Bacilli to produce cellobiose, and the second step is to convert cellobiose into glucose by a B-glucosidase expressing recombinant yeast strain. As lignocellulosic material, wood powder from industrial waste was used and the degradation of the wood powder into glucose was confirmed by following the growth curve of the microorganisms and through appropriate enzymatic assays. The second part of the study utilizes two novel technologies, Yeast Artificial Chromosome (YAC) and Bridge-Induced Translocation (BIT) to introduce new, multi-factorial genetic traits into a yeast strain, a process that would otherwise take several time-consuming and labor-intensive rounds of genetic engineering. After cloning exogenous cellulases onto a YAC vector, this was transformed into a PEP4 mutant yeast upon which BIT technology was applied. This technology allowed the research to gain two advantages; one of them was to stabilize the YAC within the yeast genome and the other one was to have increased gene expression level consequent to the translocation event. In conclusion, this work defines a successful microbial system that is able to efficiently utilize lignocellulosic material as a carbon source and a translocant yeast strain that has high level of cellulase activity

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

(no abstract

Second CLIPS Conference Proceedings, volume 1

Topics covered at the 2nd CLIPS Conference held at the Johnson Space Center, September 23-25, 1991 are given. Topics include rule groupings, fault detection using expert systems, decision making using expert systems, knowledge representation, computer aided design and debugging expert systems