Action needed to make carbon offsets from forest conservation work for climate change mitigation.

Carbon offsets from voluntary avoided-deforestation projects are generated on the basis of performance in relation to ex ante deforestation baselines. We examined the effects of 26 such project sites in six countries on three continents using synthetic control methods for causal inference. We found that most projects have not significantly reduced deforestation. For projects that did, reductions were substantially lower than claimed. This reflects differences between the project ex ante baselines and ex post counterfactuals according to observed deforestation in control areas. Methodologies used to construct deforestation baselines for carbon offset interventions need urgent revisions to correctly attribute reduced deforestation to the projects, thus maintaining both incentives for forest conservation and the integrity of global carbon accounting.

Can plant DNA barcoding be implemented in species-rich tropical regions? A perspective from São Paulo State, Brazil.

DNA barcoding helps to identify species, especially when identification is based on parts of organisms or life stages such as seeds, pollen, wood, roots or juveniles. However, the implementation of this approach strongly depends on the existence of complete reference libraries of DNA sequences. If such a library is incomplete, DNA-based identification will be inefficient. Here, we assess if DNA barcoding can already be implemented in species-rich tropical regions. We focus on the tree flora of São Paulo state, Brazil, which contains more than 2000 tree species. Using new DNA sequence data and carefully assembled GenBank accessions, we assembled 12,113 sequences from ten different regions. The ITS, rbcL, psbA-trnH, matK and trnL regions were better represented within the available sequences for São Paulo tree flora. Currently, only 58% of the São Paulo tree flora currently have at least one barcoding sequence available. However, these species represent on average 89% of the trees in São Paulo state forests. Therefore, conservation-oriented and ecological studies can already benefit from DNA barcoding to obtain more accurate species identifications. We present which taxa remain underrepresented for the São Paulo tree flora and discuss the implications of this result for other species-rich tropical regions.

Essential molecular functions associated with the circular code evolution.

A circular code is a set of trinucleotides allowing the reading frames in genes to be retrieved locally, i.e. anywhere in genes and in particular without start codons, and automatically with a window of few nucleotides. In 1996, a common circular code, called X, was identified in large populations of eukaryotic and prokaryotic genes. Hence, it is believed to be an ancestral structural property of genes. A new computational approach based on comparative genomics is developed to identify essential molecular functions associated with circular codes. It is based on a quantitative and sensitive statistical method (FPTF) to identify three permuted trinucleotide sets in the three frames of genes, a flower automaton algorithm to determine if a trinucleotide set is a circular code or not, and an integrated Gene Ontology and Taxonomy (iGOT) database. By carrying out automatic circular code analyses on a huge number of gene populations where each population is associated with a particular molecular function, it identifies 266 gene populations having circular codes close to X. Surprisingly, their molecular functions include 98% of those covered by the essential genes of the DEG database (Database of Essential Genes). Furthermore, three trinucleotides GTG, AAG and GCG, replacing three trinucleotides of the code X and called "evolutionary" trinucleotides, significantly occur in these 266 gene populations. Finally, a new method developed to analyse and quantify the stability of a set of trinucleotides demonstrates that these evolutionary trinucleotides are associated with a significant increase of the stability of the common circular code X. Indeed, its stability increases from the 1502th rank to the 16th rank after the replacement of the three evolutionary trinucleotides among 9920 possible trinucleotide replacement sets.

Frameshift signals in genes associated with the circular code.

Three sets of 20 trinucleotides are preferentially associated with the reading frames and their 2 shifted frames of both eukaryotic and prokaryotic genes. These 3 sets are circular codes. They allow retrieval of any frame in genes (containing these circular code words), locally anywhere in the 3 frames and in particular without start codons in the reading frame, and automatically with the reading of a few nucleotides. The circular code in the reading frame, noted X, which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshift genes, i. e. genes with a change of reading frame during translation. This work studies the circular code signal around their frameshift sites. Two scoring methods are developed, a function P based on this code X and a function Q based both on this code X and the 4 trinucleotides with identical nucleotides. They detect a significant correlation between the code X and the -1 frameshift signals in both eukaryotic and prokaryotic genes, and the +1 frameshift signals in eukaryotic genes.

Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes.

We developed a statistical method that allows each trinucleotide to be associated with a unique frame among the three possible ones in a (protein coding) gene. An extensive gene study in 175 complete bacterial genomes based on this statistical approach resulted in identification of 72 new circular codes. Finding a circular code enables an immediate retrieval of the reading frame locally anywhere in a gene. No knowledge of location of the start codon is required and a short window of only a few nucleotides is sufficient for automatic retrieval. We have therefore developed a factorization method (that explores previously found circular codes) for retrieving the reading frames of bacterial genes. Its principle is new and easy to understand. Neither complex treatment nor specific information on the nucleotide sequences is necessary. Moreover, the method can be used for short regions in nucleotide sequences (less than 25 nucleotides in protein coding genes). Selected additional properties of circular codes and their possible biological consequences are also discussed.

An analytical model of gene evolution with six mutation parameters: an application to archaeal circular codes.

We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64 x 64 with six substitution parameters associated with the transitions and transversions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4 x 4 and the trinucleotide mutation matrix 64 x 64 with three parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to six substitution parameters. An application of this model allows an evolutionary study of the common circular code COM and the 15 archaeal circular codes X which have been recently identified in several archaeal genomes. The main property of a circular code is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. In genes, the circular code is superimposed on the traditional genetic one. Very unexpectedly, the evolutionary model demonstrates that the archaeal circular codes can derive from the common circular code subjected to random substitutions with particular values for six substitutions parameters. It has a strong correlation with the statistical observations of three archaeal codes in actual genes. Furthermore, the properties of these substitution rates allow proposal of an evolutionary classification of the 15 archaeal codes into three main classes according to this model. In almost all the cases, they agree with the actual degeneracy of the genetic code with substitutions more frequent in the third trinucleotide site and with transitions more frequent that transversions in any trinucleotide site.

Prevalencia del consumo de tabaco en médicos residentes de pediatría en Argentina / Prevalence of tobacco use among pediatric residents in Argentina

OBJETIVOS: Determinar la prevalencia de tabaquismo en residentes de pediatría en Argentina, evaluar los factores de riesgo asociados con ese hábito y analizar la actitud preventiva de estos profesionales en relación con el consumo de tabaco por parte de sus pacientes. MÉTODOS: Se realizó un estudio transversal por encuesta mediante cuestionarios anónimos autoadministrados. Las encuestas se aplicaron en mayo de 2002 a residentes de pediatría de ocho hospitales de las provincias de Buenos Aires, Córdoba, La Plata, Mendoza y Neuquén, en la República Argentina. Las variables de estudio fueron: el sexo, la edad, el año de la residencia en curso, el número de guardias por semana, si vivía solo, si la madre o el padre fumaban, la edad en que comenzó a fumar, el lugar y las actividades del hospital en las que más fumaba, si su jefe inmediato era fumador, si había aumentado el consumo de tabaco después de ingresar a la residencia, su actitud preventiva en relación con el consumo de tabaco por parte de sus pacientes y de los padres de sus pacientes, y sus conocimientos acerca de los riesgos del tabaquismo. Se calcularon las frecuencias de las variables estudiadas y las razones de posibilidades (odds ratios,RP) y sus intervalos de confianza de 95 por ciento (IC95 por ciento). Se aplicó la regresión logística múltiple en un modelo con todas las variables predictoras posibles. El nivel de significación fue de P <0,05. RESULTADOS: Se obtuvieron 349 respuestas (98,8 por ciento de los residentes presentes en el momento de la encuesta). La prevalencia de fumadores entre los residentes de pediatría encuestados fue de 22,2 por ciento. De ellos, 38,9 por ciento admitieron fumar más que antes de incorporarse a la residencia y 63,9 por ciento identificaron a la guardia como la actividad en la que más fumaban dentro del hospital. Después de hacer ajustes en función del resto de las variables, tanto el tener madre fumadora (RP: 2,7; IC95 por ciento: 1,57 a 4,84) como el vivir solo (RP: 3,15; IC95 por ciento: 1,58 a 6,26) siguieron siendo factores de riesgo de ser fumador. Solo 26,5 por ciento respondieron que explicaban a sus pacientes los riesgos del consumo de tabaco y 23,2 por ciento que les aconsejaban que dejaran de fumar o no comenzaran, sin diferencias entre los residentes fumadores y los que no fumaban. CONCLUSIONES: La prevalencia del tabaquismo entre los médicos residentes de pediatría es elevada, aunque se asemeja a la observada en otros médicos argentinos...

Circular codes in archaeal genomes.

A new statistical method associating each trinucleotide with a frame is developed for identifying circular codes. Its sensibility allows the detection of several circular codes in the (protein coding) genes of archaeal genomes. Several properties of these circular codes are described, in particular the lengths of the minimal windows to retrieve the construction frames, a new definition of a parameter for measuring some probabilities of words generated by the circular codes, and the types of nucleotides in the trinucleotide sites. Some biological consequences are presented in Discussion.