Standards recommendations for the Earth BioGenome Project.

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Earth BioGenome Project: Sequencing life for the future of life.

Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

Land-use and climate change risks in the Amazon and the need of a novel sustainable development paradigm.

For half a century, the process of economic integration of the Amazon has been based on intensive use of renewable and nonrenewable natural resources, which has brought significant basin-wide environmental alterations. The rural development in the Amazonia pushed the agricultural frontier swiftly, resulting in widespread land-cover change, but agriculture in the Amazon has been of low productivity and unsustainable. The loss of biodiversity and continued deforestation will lead to high risks of irreversible change of its tropical forests. It has been established by modeling studies that the Amazon may have two "tipping points," namely, temperature increase of 4 °C or deforestation exceeding 40% of the forest area. If transgressed, large-scale "savannization" of mostly southern and eastern Amazon may take place. The region has warmed about 1 °C over the last 60 y, and total deforestation is reaching 20% of the forested area. The recent significant reductions in deforestation-80% reduction in the Brazilian Amazon in the last decade-opens up opportunities for a novel sustainable development paradigm for the future of the Amazon. We argue for a new development paradigm-away from only attempting to reconcile maximizing conservation versus intensification of traditional agriculture and expansion of hydropower capacity-in which we research, develop, and scale a high-tech innovation approach that sees the Amazon as a global public good of biological assets that can enable the creation of innovative high-value products, services, and platforms through combining advanced digital, biological, and material technologies of the Fourth Industrial Revolution in progress.

Muscle fiber type proportion and size is not altered in mcardle disease.

INTRODUCTION: McArdle disease is a metabolic myopathy that presents with exercise intolerance and episodic rhabdomyolysis. Excessive muscle recruitment has also been shown to be present during strenuous exercise, suggesting decreased power output. These findings could potentially be explained by either impaired contractility, decreased fiber size, or altered fiber type proportion. However, there is a paucity of data on the morphological features seen on muscle histology. METHODS: We examined muscle biopsies of patients with McArdle disease from a Spanish cohort and compared the findings with healthy controls. RESULTS: We found no significant difference in the fiber type proportion or mean fiber size between McArdle patients and controls in the biceps brachii or vastus lateralis muscles. CONCLUSIONS: No alterations in muscle fiber type proportion or size were found on muscle histology of patients with McArdle disease. Future research should focus on assessment of muscle fiber contractility to investigate the functional impairment. Muscle Nerve 55: 916-918, 2017.

Taking advantage of an old concept, "illegitimate transcription", for a proposed novel method of genetic diagnosis of McArdle disease.

PURPOSE: McArdle disease is a metabolic disorder caused by pathogenic mutations in the PYGM gene. Timely diagnosis can sometimes be difficult with direct genomic analysis, which requires additional studies of cDNA from muscle transcripts. Although the "nonsense-mediated mRNA decay" (NMD) eliminates tissue-specific aberrant transcripts, there is some residual transcription of tissue-specific genes in virtually all cells, such as peripheral blood mononuclear cells (PBMCs). METHODS: We studied a subset of the main types of PYGM mutations (deletions, missense, nonsense, silent, or splicing mutations) in cDNA from easily accessible cells (PBMCs) in 12 McArdle patients. RESULTS: Analysis of cDNA from PBMCs allowed detection of all mutations. Importantly, the effects of mutations with unknown pathogenicity (silent and splicing mutations) were characterized in PBMCs. Because the NMD mechanism does not seem to operate in nonspecific cells, PBMCs were more suitable than muscle biopsies for detecting the pathogenicity of some PYGM mutations, notably the silent mutation c.645G>A (p.K215=), whose effect in the splicing of intron 6 was unnoticed in previous muscle transcriptomic studies. CONCLUSION: We propose considering the use of PBMCs for detecting mutations that are thought to cause McArdle disease, particularly for studying their actual pathogenicity.Genet Med 18 11, 1128-1135.

Early Diagnosis of Oral Cancer and Lesions in Fanconi Anemia Patients: A Prospective and Longitudinal Study Using Saliva and Plasma.

Fanconi anemia (FA) patients display an exacerbated risk of oral squamous cell carcinoma (OSCC) and oral potentially malignant lesions (OPMLs) at early ages. As patients have defects in their DNA repair mechanisms, standard-of-care treatments for OSCC such as radiotherapy and chemotherapy, give rise to severe toxicities. New methods for early diagnosis are urgently needed to allow for treatment in early disease stages and achieve better clinical outcomes. We conducted a prospective, longitudinal study wherein liquid biopsies from sixteen patients with no clinical diagnoses of OPML and/or OSCC were analyzed for the presence of mutations in cancer genes. The DNA from saliva and plasma were sequentially collected and deep-sequenced, and the clinical evaluation followed over a median time of approximately 2 years. In 9/16 FA patients, we detected mutations in cancer genes (mainly TP53) with minor allele frequencies (MAF) of down to 0.07%. Importantly, all patients that had mutations and clinical follow-up data after mutation detection (n = 6) developed oral precursor lesions or OSCC. The lead-time between mutation detection and tumor diagnosis ranged from 23 to 630 days. Strikingly, FA patients without mutations displayed a significantly lower risk of developing precursor lesions or OSCCs. Therefore, our diagnostic approach could help to stratify FA patients into risk groups, which would allow for closer surveillance for OSCCs or precursor lesions.

Polymorphisms influencing muscle phenotypes in North-African and Spanish populations.

AIM: The purpose of this study was to determine the allelic and genotypic frequency distribution of the C34T mutation in the muscle isoform of the adenosine monophosphate deaminase 1 (AMPD1) gene and of the missense substitution K153R in the myostatin (GDF8) gene in one Spanish and two North African populations. METHOD: One sample of 98 individuals was genotyped from the South of Spain (Alpujarra) and two samples from Morocco (77 Berbers and 78 Arabs). RESULTS: The frequency of the AMPD1 C34T mutation was lower in Berbers (0.071) compared with the Alpujarra cohort (0.153, p = 0.018). The GDF8 K153R substitution showed little variability among the three cohorts. CONCLUSIONS: Studies with larger cohorts and other ethnic groups are needed to corroborate that there does not exist any major variability in the genotype distribution of genes associated with muscle phenotypes in the South-Eastern Mediterranean area.

Influence of Contact Plateaus Characteristics Formed on the Surface of Brake Friction Materials in Braking Performance through Experimental Tests.

This work applies a procedure for analysis and characterization of the surface of brake friction materials, correlating them with the tribological and thermal properties achieved in different vehicle braking conditions. Experiments were performed in a vehicle under two real conditions of braking operation, simulated flat track descent and emergency braking. Characteristics of the plates formed on the surfaces of the friction materials were analyzed by scanning electron microscopy (SEM) and correlated with the performance during braking, as measured by the coefficient of friction at the interface of the friction pair and temperature. As a result, the formation of the primary and secondary plateaus in these two different braking operating conditions was observed, and the relationship between the characteristics of the plateaus formed on the surface and the surface roughness parameters and performance measurements during braking.

[Heat health warning systems: possibilities of improvement]. / Posibilidades de mejora en los planes de prevención frente al exceso de temperaturas.

In the summer of 2003 the temperatures reached were responsible for a large number of deaths in Europe. A year after this fact, many countries had implemented some sort of plan of prevention against excessive temperatures. Plans that had already shown its ability to prevent a large proportion of avoidable mortality in other latitudes. Since then, a lot of papers have been published providing new data on health effects of a heat wave, which can help increase the efficiency of these prevention plans. Knowing the weather conditions at risk, defining "heat wave" or to take into account the time that the plan should be active from the study of the relationship between temperature and their effects on health, to identify weather patterns that modulate the relationship between temperature and mortality, locate the profile of people at risk or to develop protocols for action as accurately as possible and based on scientific knowledge are elements drawn from studies carried on in recent years that should be taken into account.

Concomitant and controlled release of furazolidone and bismuth(III) incorporated in a cross-linked sodium alginate-carboxymethyl cellulose hydrogel.

The combination of bismuth(III) citrate and the antibiotic furazolidone (FDZ) results in a synergetic effect on Helicobacter pylori eradication. However, the problems associated with their oral administration are challenges to overcome. Thus, in the present study, sodium alginate (SA)/carboxymethyl cellulose (CMC) blend hydrogels (SC) were developed for concomitant and controlled release of furazolidone and bismuth(III). The blank formulation (SCblank) and the three drug-loaded hydrogels (SCFDZ, SCBi, and SCFDZ-Bi) were prepared by casting method and characterized by infrared spectroscopy, scanning electron microscopy, differential scanning calorimetry, and X ray powder diffraction analyses. The swelling equilibrium and cumulative release amounts of FDZ and Bi3+ have indicated distinct behaviors of the hydrogels to different pH values. The bismuth-containing sample (SCFDZ-Bi) presents more resistance to degradation on a neutral solution and shows more suitable properties for controlled drug release than the sample without bismuth (SCFDZ). Microbiological studies, using Escherichia coli as a model, show bacteria viability reduction in presence of the drug-loaded samples. The developed system containing furazolidone and bismuth(III) appears to be promising for oral administration with concomitant and controlled release of these drugs aimed at the pharmacological treatment of gastrointestinal disorders.

Expression of the muscle glycogen phosphorylase gene in patients with McArdle disease: the role of nonsense-mediated mRNA decay.

Nearly 35% of all mutations identified in the muscle glycogen phosphorylase gene (PYGM) in patients with McArdle disease result in premature termination codons (PTCs), particularly the p.R50X mutation. The latter accounts for more than 50% of the mutated alleles in most Caucasian patient populations. Mutations resulting in PTC could trigger the degradation of mRNA through a mechanism known as nonsense mediated decay (NMD). To investigate if NMD affects the levels of transcripts containing PYGM mutations, 28 Spanish patients with McArdle disease, harboring 17 different mutations with PTCs in 77% of their alleles, were studied. Transcripts levels of PYGM were measured and sequenced. We assessed that 92% of patients showed NMD. The most frequent mutation (p.R50X) elicited decay in all the genotypes tested. Other PTC producing mutations resulting in NMD were: p.L5VfsX22, p.Q73HfsX7, p.E125X, p.N134KfsX161, p.W388SfsX34, p.R491AfsX7, and p.D534VfsX5. Located in the last exon, the mutation p.E797VfsX19 was not affected by NMD. Missense mutations did not appear to be affected by NMD. In the cDNA sequences they appeared as homozygous, despite being heterozygous in the genomic DNA sequences. Exceptions to the rules governing NMD were found in the mutations p.A704 V and p.K754NfsX49.

Vacuum Thermoforming Process: An Approach to Modeling and Optimization Using Artificial Neural Networks.

In the vacuum thermoforming process, the group effects of the processing parameters, when related to the minimizing of the product deviations set, have conflicting and non-linear values which make their mathematical modelling complex and multi-objective. Therefore, this work developed models of prediction and optimization using artificial neural networks (ANN), having the processing parameters set as the networks' inputs and the deviations group as the outputs and, furthermore, an objective function of deviation minimization. For the ANN data, samples were produced in experimental tests of a product standard in polystyrene, through a fractional factorial design (2k-p). Preliminary computational studies were carried out with various ANN structures and configurations with the test data until reaching satisfactory models and, afterwards, multi-criteria optimization models were developed. The validation tests were developed with the models' predictions and solutions showed that the estimates for them have prediction errors within the limit of values found in the samples produced. Thus, it was demonstrated that, within certain limits, the ANN models are valid to model the vacuum thermoforming process using multiple parameters for the input and objective, by means of reduced data quantity.

[Trends in effects of maximum temperatures on organic-cause mortality in Castile-La Mancha, Spain from 1975 to 2003]. / Evolución de los efectos de las temperaturas máximas sobre la mortalidad por causas orgánicas en castilla--La Mancha de 1975 a 2003.

BACKGROUND: Non-lineal temperature-mortality relationship varies depending on the characteristics of the designated study geographic zone. In given places, a growing level of economic development has led to lesser influence of environmental variables on mortality. This paper analyzes trends in the association between maximum temperatures and organic-cause mortality from 1975 to 2003 in Castile-La Mancha (Spain). METHODS: Daily maximum temperatures and organic-cause mortality data were divided into 3 time period: 1975-1984, 1985-1994 and 1995-2003. After data pre-whitening by applying ARIMA model estimated for the daily maximum temperature series, we calculate cross-correlation functions between residuals of temperature and mortality, 7 days lagged for summer, 15 for cold months, and comparing its correlation coefficients. RESULTS: We observe an increasing number of significant lags during the warm season (p < 0.05) between first and second decades studied in regional overall but with some provincial differences. In the third study period the number of significant lags varies slightly, although cross correlation coefficients were significantly upward (p < 0.05) at lag 3 in the entire region and Toledo in particular. CONCLUSIONS: Maximum temperature and mortality by organic cause association became more extensive and intense since 1975-1984 decade in Castile-La Mancha. The aging of regional population could offset the probable beneficial effect of economic growth on this relationship. No appreciable time trends are found in cold months.

[Treatment and temperature series study for use in public health. The case of Castilla-La Mancha, Spain]. / Tratamiento y estudio de series de temperatura para su aplicación en salud pública. El caso de Castilla- La Mancha.

BACKGROUND: Numerous articles relate atmospheric variables to health indicators. In large regions, such as Castilla-La Mancha, it may be necessary to divide the region into areas in terms of the atmospheric variables available by selecting a representative weather station for each zone. This article focuses on analyzing the daily temperature data from numerous Castilla La Mancha observatories and reducing the number thereof to a few representative stations for being used in studies relating atmospheric variables to health indicators in this region. METHODS: Castilla-La Mancha weather stations were selected in terms of the number of years available and missing data. After filling in the gaps in the selected series, to detect any possible discontinuities and to homogenize the series, the daily temperature data is used in hierarchical cluster and factorial analyses by principal components. RESULTS: Factorial analyses extract one single factor by using the maximum, mean or minimum temperature series. For the maximum temperatures, this factor explains 93.45% of the variance, with an eigenvalue of 39.249. The "Compuesta" station in Toledo shows correlation coefficients in the principal components matrix of 0.987, 0.991 and 0.981 respectively for the maximum, mean and minimum temperature series. CONCLUSIONS: Castilla-La Mancha is an isoclimatic region in terms of the temperature, the "Compuesta" station in Toledo being selected as the representative station for the region for public health studies. The results afford the possibility of conducting studies broken down into small units such as the provinces, with the stations in the government capitals as a reference.

The A8296G mtDNA mutation associated with several mitochondrial diseases does not cause mitochondrial dysfunction in cybrid cell lines.

Transmitochondrial cybrid cell lines homoplasmic for the A8296G mtDNA transition, a mutation associated with several mitochondrial diseases, have a normal oxidative phosphorylation function, as shown by oxygen consumption, lactate production, respiratory enzyme activities, and growth using galactose as the only source of energy. The synthesis of mitochondrial proteins is also similar in mutant and wild-type cybrids. Our results suggest that the A8296G mutation is a polymorphism and reinforce the necessity of performing functional studies to assess the pathogenicity of mtDNA mutations.

[Legionella pneumophila pneumonia associated with the use of a home humidifier in an immunocompetent girl]. / Neumonía por Legionella pneumophila asociada al uso de un humidificador doméstico en una niña inmunocompetente.

BACKGROUND AND OBJECTIVES: Legionellosis is an uncommon cause of pneumonia in children and even more exceptionally in healthy children. The purpose of this study is to describe the procedure which led to the identification of an unusual source of legionella infection, in a healthy girl, and highlight the need to adopt preventive measures. METHODOLOGY AND RESULTS: A 4-year old girl without any risk factors was diagnosed of pneumonia caused by Legionella pneumophila serogroup 1. After investigating the environment, it was found that the source of the transmission was a home humidifier. CONCLUSIONS: Despite the fact that this equipment is classified with a low probability of spreading legionella, a lack of cleanliness and maintenance of these machines can increase the risk of transmission of the bacteria. Therefore, healthcare professionals must give adequate advice to their patients about the care of this equipment and how to use these machines properly.

[Evaluation of the efficacy of the sewage treatment plant of Toledo, Spain in the elimination of drugs of abuse and the estimation of consumption]. / Estimación del consumo de drogas de abuso y sus metabolitos a partir de su presencia en el agua residual de Talavera de la Reina y en el río Tajo.

BACKGROUND: in the last years, the presence of new contaminants in water has been rising. There are only few studies which analyze such presence. The aims were to determine the occurrence of drugs of abuse and their metabolites in the influent and effluent of the Sewage Treatment Plant (STP) in Talavera de la Reina, and the River Tagus, as well as to evaluate the STP removal efficiency in the elimination of these substances and to estimate the consumption of drugs in Talavera. METHODS: whe samples were taken on June 28, 2010. The presence of 5 groups of drugs (10 drugs of abuse and 9 metabolites) was quantified. The efficiency was calculated from the percentage of reduction of the concentration in the influent and effluent of the STP. Drug consumption was calculated from influent concentrations. Using a specific methodology, based on the assumption the drugs after they are consumed and metabolized in the human body are excreted as parent compounds or metabolites. Whose metabolic pathways are known, and the amount of drug or metabolite quantified corresponds to the dose consumed. RESULTS: ten substances were detected. In all sampling points appeared: Benzoiclegonina (BE) (cocaine metabolite), ephedrine, methadone and its metabolite EDDP. The highest concentrations were of BE (239 ng/L), and THC-COOH (35 ng/L), both in influent. In the Tagus River, the highest concentrations were of BE (5.38 ng/L) and EDDP (4.4 ng/L). The STP removal efficiency was up to 80% for all substances except for methadone (which was zero) and EDDP (increasing to leave the STP). The estimated consumption shows that the most consumed substances were cannabis (1.88 grams / day) and cocaine (0.46 grams / day). CONCLUSION: the presence of drugs of abuse in River Tagus in Talavera demonstrates that these substances are not eliminated completly by STPs. Drug consumption estimate indicates that the population of Talavera mainly consumed cannabis and cocaine. Thus this methodology can complement epidemiological surveys.

McArdle disease does not affect skeletal muscle fibre type profiles in humans.

Patients suffering from glycogen storage disease V (McArdle disease) were shown to have higher surface electrical activity in their skeletal muscles when exercising at the same intensity as their healthy counterparts, indicating more muscle fibre recruitment. To explain this phenomenon, this study investigated whether muscle fibre type is shifted towards a predominance in type I fibres as a consequence of the disease. Muscle biopsies from the Biceps brachii (BB) (n = 9) or Vastus lateralis (VL) (n = 8) were collected over a 13-year period from male and female patients diagnosed with McArdle disease, analysed for myosin heavy chain (MHC) isoform content using SDS-PAGE, and compared to healthy controls (BB: n = 3; VL: n = 10). All three isoforms were expressed and no difference in isoform expression in VL was found between the McArdle patients and healthy controls (MHC I: 33±19% vs. 43±7%; MHC IIa: 52±9% vs. 40±7%; MHC IIx: 15±18% vs. 17±9%). Similarly, the BB isoform content was also not different between the two groups (MHC I: 33±14% vs. 30±11%; MHC IIa: 46±17% vs. 39±5%; MHC IIx: 21±13% vs. 31±14%). In conclusion, fibre type distribution does not seem to explain the higher surface EMG in McArdle patients. Future studies need to investigate muscle fibre size and contractility of McArdle patients.

MPV17 Mutations Causing Adult-Onset Multisystemic Disorder With Multiple Mitochondrial DNA Deletions.

OBJECTIVE To identify the cause of an adult-onset multisystemic disease with multiple deletions of mitochondrial DNA (mtDNA). DESIGN Case report. SETTING University hospitals. PATIENT A 65-year-old man with axonal sensorimotor peripheral neuropathy, ptosis, ophthalmoparesis, diabetes mellitus, exercise intolerance, steatohepatopathy, depression, parkinsonism, and gastrointestinal dysmotility. RESULTS Skeletal muscle biopsy revealed ragged-red and cytochrome- c oxidase-deficient fibers, and Southern blot analysis showed multiple mtDNA deletions. No deletions were detected in fibroblasts, and the results of quantitative polymerase chain reaction showed that the amount of mtDNA was normal in both muscle and fibroblasts. Exome sequencing using a mitochondrial library revealed compound heterozygous MPV17 mutations (p.LysMet88-89MetLeu and p.Leu143*), a novel cause of mtDNA multiple deletions. CONCLUSIONS In addition to causing juvenile-onset disorders with mtDNA depletion, MPV17 mutations can cause adult-onset multisystemic disease with multiple mtDNA deletions.