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Hereditary angioedema due to pathogenic FXII variants (HAE-FXII) is a rare dominant disease caused by increased activation of the plasma contact system. The most prevalent HAE-FXII variant, c.1032C > A p.Thr309Lys (FXII309Lys), results in a smaller FXII protein with increased sensitivity to fluid-phase activation by poorly understood mechanisms. We aimed to investigate the functionality of the FXII309Lys variant in 33 HAE-FXII patients, 25 healthy controls and 46 patients with congenital disorders of glycosylation (CDG). Activation of the plasma contact system was assessed by western blot and amidolytic assay in basal conditions or after treatment with either artificial or physiological activators. Recombinant wild-type and FXII309Lys variants were expressed in S2 insect (Drosophila) cells. Amidolytic and fibrin generation assays were performed in fresh plasma samples. FXII309Lys samples exhibited an increased electrophoretic mobility comparable with N-glycan-deficient FXII from CDG patients and asialo-FXII generated by neuraminidase treatment. They presented increased sensitivity to activation by dextran sulphate and silica which resulted in the generation of an aberrant 37-kDa heavy chain. We did not observe increased susceptibility of FXII309Lys to proteolysis by exogenous or tPA-generated plasmin. However, both exogenous and endogenous thrombin cleaved the FXII309Lys variant, releasing a 37-kDa fragment and resulting in enhanced proteolytic activation on the fluid phase. This model supports a sequential proteolytic activation process involving thrombin priming of FXII309Lys, followed by kallikrein cleavage and generation of active βFXIIa. The present results and the observation that angioedema episodes in HAE-FXII patients occur predominantly during hypercoagulable situations suggest a key role for thrombin.

Recurrent problems have been observed for biomass measurement in tree sprouts, mainly dueto differences in patterns of biomass distribution and the bias generated by using models for mature trees.The objective of this research was to evaluate models to estimate aboveground biomass in sprouts from two-year-old stumps of Short Rotation Woody Crops (SRWC) used for energetic purposes. The study was conducted in Central Chile (Bío-Bío region) under a complete block design and four replications.Three plant species were included: Eucalyptus globulus, E. denticulata, and Acacia dealbata, established in three population densities (5,000, 10,000 and 15,000 trees per ha). Two groups of nonlinear models wereused on three independent variables: root collar diameter (squared mean of two dominant stems), height (mean of two dominant stems) and number of epicormic stems. In the allometric model, the total aboveground biomass and the aboveground biomass by component were explained as the product of the mean square of the root collar diameter, mean height of the two dominant new sprouts and total number of epicormic sprouts as the predictive variable. Values of coefficient of determination (R2) ranged from 0.78 to 0.95 and RMSE ranged from 168 to 913 g. The species of E. globulus showed higher RMSE for biomass estimation in the all components except the branch component. The inclusion of dummy variables to identify the differences in each parameter of the models explained the seasonalityof the biomass accumulation in tree sprouts at 10, 21, and 31 months of age, improving the model goodness of fit RMSE by 27%. Accurate prediction of sprouts aboveground biomass was obtained by the models only evaluating the two dominant epicormic sprouts in the stump, avoiding the need of individual sprouts evaluation or using destructive methods for biomass measurement.

El manejo forestal a través de la aplicación de tratamientos silvícolas adecuados permite lograr la persistencia, el rendimiento sostenido y la máxima producción de los bosques. El objetivo de este trabajo fue evaluar el incremento en volumen fustal de árboles de Pinus durangensis, a partir del análisis de los anillos de crecimiento mediante la técnica del análisis troncal en rodales sometidos a cuatro tratamientos silvícolas; los cuales fueron cortas de regeneración con árboles Padre (realizada en 2007), matarrasa, selección y de aclareo aplicados en el año 2010. Se estudiaron 16 árboles muestra de Pinus durangensis recolectados en sitios de 100 m2, distribuidos al azar por cada tratamiento. Para el análisis troncal, por individuo se obtuvo una rodaja a la base, otra a 1.3 m sobre el nivel del suelo y posteriormente cada metro hasta llegar a la punta. Se estimó el diámetro y la altura de los árboles cada dos anillos de crecimiento y se estimó el volumen, para finalmente conocer los incrementos (ICA e IMA) en intervalos de dos años. Los resultados de la prueba no paramétrica de Kruskal Wallis mostraron diferencias significativas (p < 0.05) en el ICA e IMA en la mayoría de los tratamientos silvícolas evaluados. La matarrasa resultó ser la práctica con los mayores valores de ICA e IMA para todas las edades estudiadas.

Background Congenital disorders of glycosylation are rare inherited diseases affecting many different proteins. The lack of glycosylation notably affects the hemostatic system and leads to deficiencies of both procoagulant and anticoagulant factors. Objective To assess the hemostatic balance in patients with multiple coagulation disorders by using a thrombin generation assay. Method We performed conventional coagulation assays and a thrombin generation assay on samples from patients with congenital disorder of glycosylation. The thrombin generation assay was performed before and after activation of the protein C system by the addition of soluble thrombomodulin. Results A total of 35 patients were included: 71% and 57% had low antithrombin and factor XI levels, respectively. Protein C and protein S levels were abnormally low in 29% and 26% of the patients, respectively, whereas only 11% displayed low factor IX levels. Under baseline conditions, the thrombin generation assay revealed a significantly higher endogenous thrombin potential and thrombin peak in patients, relative to controls. After spiking with thrombomodulin, we observed impaired involvement of the protein C system. Hence, 54% of patients displayed a hypercoagulant phenotype in vitro. All the patients with a history of stroke-like episodes or thrombosis displayed this hypercoagulant phenotype. Conclusion A thrombin generation assay revealed a hypercoagulant in vitro phenotype under baseline condition; this was accentuated by impaired involvement of the protein C system. This procoagulant phenotype may thus reflect the risk of severe vascular complications. Further research will have to determine whether the thrombin generation assay is predictive of vascular events.

Severe infectious diseases are often characterized by an overwhelming and unbalanced systemic immune response to microbial infections. Human antithrombin (hAT) is a crucial coagulation inhibitor with anti-inflammatory activities. Here we identify three hAT-binding proteins (CD13, CD300f and LRP-1) on human monocytes that are involved in blocking the activity of nuclear factor-κB. We found that the modulating effect is primarily restricted to the less abundant β-isoform (hβAT) of hAT that lacks N-glycosylation at position 135. Individuals with a mutation at this position have increased production of hβAT and analysis of their blood, which was stimulated ex vivo with lipopolysaccharide, showed a decreased inflammatory response. Similar findings were recorded when heterozygotic mice expressing hAT or hβAT were challenged with lipopolysaccharide or infected with Escherichia coli bacteria. Our results finally demonstrate that in a lethal E. coli infection model, survival rates increased when mice were treated with hβAT one hour and five hours after infection. The treatment also resulted in a reduction of the inflammatory response and less severe organ damage.

Inherited antithrombin (AT) deficiency, with prevalence in the general population ranging 0.02-0.17%, is an autosomal dominant disorder associated with a high risk of venous thromboembolism. In most cases, deficiency is caused by mutations in the AT-coding gene (SERPINC1). Only 24 splicing defects have been described causing AT deficiency, all affecting exon flanking regions. The aim of the current study was to characterize the mutations underlying AT deficiency in 10 venous thromboembolism Polish patients aged 42.9 (14-63) years. Whole SERPINC1 gene sequencing was done by next generation sequencing methods. Eight cases had mutations previously described. However, we identified two new intronic mutations that might affect the correct splicing of exon 6 according to in-silico predictions: c.1154-1 G>C, which strongly disturbs the acceptor sequence and c.1219-534 A>G, a deep intronic mutation that might generate a cryptic donor sequence; both might compete with the wild-type donor sequence and explain the associated moderate AT deficiency of carriers. In conclusion, we show the molecular base of AT deficiency in 10 new Polish patients, including two novel SERPINC1 gene mutations potentially affecting splicing.

TO THE EDITOR: Factor XI (FXI) is a key element for the amplification of thrombin generation, which participates in the contact pathway. This explains why FXI deficiency has minor physiological relevance but protects against thrombotic events, supporting FXI as an excellent target for

El preacondicionamiento mediante estrés hídrico favorece los mecanismos de resistencia a la sequía de los árboles una vez plantados. Se realizó un ensayo con el objetivo de determinar el efecto de tres condiciones de estrés hídrico a través de riego cada 48, 144 y 288 horas, en el preacondicionamiento de plantas de nueve meses de Pinus cooperi producidas en vivero, en contenedores de 170 mL y con sustrato compuesto por turba (55%), vermiculita (24%) y agrolita (21%). Los tratamientos se distribuyeron en un diseño experimental completamente al azar, con tres repeticiones y 108 individuos en total. El ensayo constó de tres ciclos de doce días cada uno y se realizaron cuatro evaluaciones de potencial hídrico por ciclo; además, 36 días después del inicio, se registró el crecimiento morfológico de las plantas. El potencial hídrico mostró diferencias estadísticas significativas (p

Background Hereditary antithrombin deficiency is a rare autosomal-dominant disorder predisposing to recurrent venous thromboembolism (VTE). To date, only two founder mutations have been described. Objectives We investigated the antithrombin p.Thr147Ala variant, found in 12 patients of African origin. This variant is known as rs2227606 with minor allele frequency of 0.5% in Africans and absent in Europeans. A possible founder effect was investigated. Methods Phenotypical characterization was established through immunological and functional methods, both under basal and stress conditions. Recombinant antithrombin molecules were constructed by site-directed mutagenesis and expressed in HEK-293T cells. Secreted antithrombin was purified and functionally characterized. Structural modeling was performed to predict the impact of the mutation on protein structure. A novel nanopore sequencing approach was used for haplotype investigation. Results Ten patients experienced VTE, stroke, or obstetric complications. Antithrombin antigen levels and anti-IIa activity were normal or slightly reduced while anti-Xa activity was reduced with only one commercial assay. On crossed immunoelectrophoresis, an increase of antithrombin fractions with reduced heparin affinity was observed under high ionic strength conditions but not under physiological conditions. The recombinant p.Thr147Ala protein displayed a reduced anti-Xa activity. Structural modeling revealed that residue Thr147 forms three hydrogen bonds that are abolished when mutated to alanine. The investigated patients shared a common haplotype involving 13 SERPINC1 intragenic single nucleotide polymorphisms. Conclusion Antithrombin p.Thr147Ala, responsible for antithrombin type II heparin binding site deficiency, is the first founder mutation reported in people of African ancestry. This study further emphasizes the limitations of commercial methods to diagnose this specific subtype.

Aims: Traditional quantitative approaches to forest classification are based on differences in species abundance or incidence among communities. In these approaches, all species are regarded as biologically equidistant regardless of the biological heterogeneity. The objective of the study is to evaluate the potential of the “Discriminating Avalanche” approach, which integrates species abundance and biological heterogeneity, as a new basis for forest classification. Location: China, India, Iran, Ukraine, Germany, Italy, Mexico, Peru, and South Africa. Method: We illustrate our approach using a set of 35 large tree-mapped forest plots from various regions of the world. Our dissimilarity matrices, which integrate species abundance with biological heterogeneity, are compared with the standard Bray–Curtis and Whittaker dissimilarity indices, and provide the quantitative basis for a hierarchical cluster analysis. Results: Four distinct groups of forests were identified using the proposed forest dissimilarity matrix. Afro-montane forests from South Africa constitute a first group. A second group includes temperate deciduous broad-leaved forests dominated by oak (Quercus) and beech (Fagus) from Europe and China. Conifer-dominated forests constitute a third group. The remaining forests constitute the fourth group. Conclusion: Biological heterogeneity provides a practical basis for vegetation classification. The results of this study, based on a variety of temperate and tropical forests, suggest that a measure of biological dissimilarity based on evolutionary and morphological differences among species is more effective than the traditional species abundance-based approaches to classify an arbitrary set of plant communities. This approach promises greater refinement and consistency in ecological classification. In particular, it has advantage in classifying forests along large geographic scales in situations of high beta diversity and species turnover.

Estimating tree volume components is an essential element in sustainable forest management. Compatible taper and merchantable outside-bark volume systems based on volume ratio models were globally fitted to four pine species (reduced models) with the aim to select the best reduced model and to fit it with dummy variables and additive effects using Pinus pseudostrobus Lindl as a base species. The study was carried out in the northern mountains of Oaxaca, Mexico. To fit the taper, merchantable volume, stem volume, branch volume, and total tree volume (stem volume and branch volume) equations, a taper dataset of 222, 230, 245, and 333 trees of Pinus douglasiana Mart&iacute, nez (Pd), Pinus oaxacana Mirov (Po), Pinus patula Schltd (Pp), and Pinus pseudostrobus Lindl (Pps), respectively, was used. In general, the compatible systems explained more than 97% in the observed variability for the four studied components: outside-bark diameter (d), merchantable outside-bark volume (Vm), stem outside-bark volume (Vs), and total tree volume (Vt). Alternatively, more than 52% of the observed variability for branch volume (Vb) was also explained. The developed compatible systems based on volume ratio models are a simple and consistent alternative for estimating the outside-bark diameter and variable outside-bark volume, as well as the components of commercial species for uneven-age and mixed-species forests in Oaxaca, Mexico.

During platelet activation, arachidonic acid (AA) is released from membrane phospholipids and metabolized to thromboxane A2 (TXA2) through the actions of cyclooxygenase-1 (COX-1) and TXA2 synthase. Note, TXA2 binds to the platelet TXA2 receptor, causing shape change, secretion and platelet aggregation.1 Also, COX-1 (599aa; 70 kDa) has cyclooxygenase and peroxidase activities and it is functionally active as a homodimer, with each COX-1 monomer consisting of four highly conserved domains: an N-terminal signal peptide, a dimerization domain, a membrane-binding domain (MBD) and a large C-terminal catalytic domain2 (Figure 1A). Irreversible COX-1 inhibition by aspirin is a widely established anti-platelet therapy in cardiovascular disease., Fundación Mutua Madrileña, Grant/Award Number: AP172142019; Fundación Séneca, Grant/Award Number: 19873/GERM/15; Gerencia Regional de Salud, Grant/Award Numbers: 1647/A/17, 2061A/19; Instituto de Salud Carlos III (ISCIII) & Feder, Grant/Award Numbers: CB15/00055, PI17/01966, PI18/00598, PI20/00926, PI17/01311; Junta de Castilla y León; British Heart Foundation, Grant/Award Number: PG/17/40/33028; Ayuda a Grupos de Trabajo en Patología Hemorrágica; Premio López Borrasca 2019; Sociedad Española de Trombosis y Hemostasia.

N-linked glycosylation is a crucial post-translational modification involved in protein folding, function, and clearance. N-linked glycosylation is also used therapeutically to enhance the half-lives of many proteins. Antithrombin, a serpin with four potential N-glycosylation sites, plays a pivotal role in hemostasis, wherein its deficiency significantly increases thrombotic risk. In this study, we used the introduction of N-glycosylation sites as a tool to explore what effect this glycosylation has on the protein folding, secretion, and function of this key anticoagulant. To accomplish this task, we introduced an additional N-glycosylation sequence in each strand. Interestingly, all regions that likely fold rapidly or were surrounded by lysines were not glycosylated even though an N-glycosylation sequon was present. The new sequon in the strands of the A- and B-sheets reduced secretion, and the B-sheet was more sensitive to these changes. However, the mutations in the strands of the C-sheet allowed correct folding and secretion, which resulted in functional variants. Therefore, our study revealed crucial regions for antithrombin secretion and could potentially apply to all serpins. These results could also help us understand the functional effects of natural variants causing type-I deficiencies.

The identification and characterization of structural variants (SVs) in clinical genetics have remained historically challenging as routine genetic diagnostic techniques have limited ability to evaluate repetitive regions and SVs. Long-read whole-genome sequencing (LR-WGS) has emerged as a powerful approach to resolve SVs. Here, we used LR-WGS to study 19 unrelated cases with type I Antithrombin Deficiency (ATD), the most severe thrombophilia, where routine molecular tests were either negative, ambiguous, or not fully characterized. We developed an analysis workflow to identify disease-associated SVs and resolved 10 cases. For the first time, we identified a germline complex rearrangement involved in ATD previously misclassified as a deletion. Additionally, we provided molecular diagnoses for two unresolved individuals that harbored a novel SINE-VNTR-Alu retroelement insertion that we fully characterized by de novo assembly and confirmed by PCR amplification in all affected relatives. Finally, the nucleotide-level resolution achieved for all the SVs allowed breakpoint analysis, which revealed a replication-based mechanism for most of the cases. Our study underscores the utility of LR-WGS as a complementary diagnostic method to identify, characterize, and unveil the molecular mechanism of formation of disease-causing SVs, and facilitates decision making about long-term thromboprophylaxis in ATD patients.

BackgroundForest plantations play an important role in carbon sequestration, helping to mitigate climate change. In this study, survival, biomass, growth rings and annual carbon content storage were evaluated in a mixedPinus durangensisandP. cooperiplantation that was established after a clear-cutting. The plantation is eight years old and covers an area of 21.40 ha.MethodsSixteen sites of 100 m2were distributed randomly. At each site, two trees distributed proportionally to the diametric categories were destructively sampled (one per tree species). Two cross-sections were cut from each tree: The first at the base of the stump and the second at 1.30 m. The width of tree rings of the first cross-section was measured using a stereoscopic microscope with precision in microns (µm). The year-by-year basal diameter of each tree was recorded and biomass and carbon content was estimated using allometric equations.ResultsThe estimated survival was 75.2%. The results of the ANOVA showed significant differences between the year-by-year width records of tree rings, the highest value corresponding to the fifth year. The average carbon sequestration per year is 0.30 kg for both studied tree species.ConclusionsP. durangensisandP. cooperiplantations adapt and develop well in Durango forests when they are established in areas that are subjected to clear-cutting.

Antecedentes y Objetivos: El manejo forestal ocasiona cambios en la composición, estructura y funcionamiento del bosque. El objetivo de este estudio fue comparar la estructura de especies arbóreas en un periodo de 10 años en un bosque de Durango, México. Métodos: Los datos provienen de árboles con DAP mayor o igual a 7.5 cm (a una altura >1.3 m), ubicados en sitios permanentes que fueron evaluados en intervalos de cinco años (2007, 2012 y 2017). Se definieron tres estratos de altura para cada año de medición, bajo la metodología del índice de perfil vertical (A) de Pretzsch tomando en cuenta la altura mayor de cada medición. En cada estrato se evaluó la estructura a través del índice de valor de importancia (IVI), la diversidad alfa (α) con la riqueza de especies (S) y el índice de Shannon-Wiener (H’). Todas las variables dasométricas por estrato de cada medición se compararon con un ANOVA de un factor para determinar la existencia de diferencias estadísticamente significativas entre evaluaciones. Resultados clave: Aunque hubo un aumento en el área basal, el volumen y la cobertura de 2007 a 2017, este no fue estadísticamente significativo. Los estratos II y III presentaron el mayor aumento en el área basal y el volumen. La cobertura fue superior a 100%, presentando mejor contribución el estrato III. La composición de especies fue similar en las tres mediciones, siendo el estrato III el más diverso. Pinus durangensis fue la especie de mayor importancia ecológica en los estratos I y II, mientras que Quercus sideroxyla presentó relevancia alta en el III. Conclusiones: La comparación realizada en un periodo de 10 años (2007-2017) permitió determinar que la vegetación arbórea de la comunidad evaluada se mantiene sin cambios respecto a la diversidad de especies, mientras que el área basal y el volumen tienden a aumentar.

La estructura espacial refleja el patrón de disposición de los árboles sobre el terreno y es un elemento básico para entender la dinámica de los ecosistemas forestales. El objetivo de la presente investigación fue evaluar las características estructurales bivariadas de cinco asociaciones diferentes de bosques de Pinus durangensis, identificando las similitudes y diferencias en la distribución bivariada de uniformidad de ángulos, dominancia y mezcla. Los datos provienen de cinco sitios cuadrados con superficie de 2500 m2, establecidos cada uno en diferentes bosques de P. durangensis en la Sierra Madre Occidental. Para cada sitio se determinó altura promedio, diámetro promedio y cobertura de copa, así como índices de mezcla de especies, uniformidad de ángulos y dominancia. Los índices se combinaron dos a dos para obtener tres distribuciones bivariantes. El bosque puro de P. durangensis presentó los individuos con mayor altura, mientras que el mayor diámetro fue para la asociación con P. teocote. El índice de mezcla (Mi) indica que solo en el bosque puro existe una baja mezcla de especies. El índice de uniformidad de ángulos (Wi) muestra que los árboles, de manera general, tienen una distribución aleatoria. Los valores de dominancia (Ui) muestran que en todos los sitios existen todas las clases sociales representadas de manera equitativa. Los índices y sus combinaciones describen adecuadamente la distribución espacial de los árboles y su relación con sus vecinos más cercanos. La información obtenida de la combinación de las variables estructurales contribuye a mejorar la comprensión de la estructura espacial del bosque y contribuye a la regulación de la intensidad de corta y garantizar una gestión sostenible. The spatial structure reflects the pattern of arrangement of trees on the ground and is a basic element to understand the dynamics of forest ecosystems. The objective of the present investigation was to evaluate the bivariate structural characteristics of five different associations of Pinus durangensis forests, identifying the similarities and differences in the bivariate distribution of uniformity of angles, dominance and mingling. The data comes from five quadrate sites with an area of 2500 m2, each established in different forests of P. durangensis in the Sierra Madre Occidental. For each site, the average height, average diameter and crown coverage were determined, as well as the species mingling index, angle uniformity and dominance indexes. The indices were combined two to two to obtain three bivariate distributions. The pure forest of P. durangensis presented individuals with higher height, while the largest diameter was found in the association with P. teocote. The mingling index (Mi) indicates that only in the pure forest there is a low species mingling. The uniformity angle index (Wi) shows that trees generally present a random distribution. The values of dominance (Ui) show that in all the sites there are all the social classes represented in an equitable way. The indexes and their combinations adequately describe the spatial distribution of the trees and their relationship with their closest neighbors. The information obtained from the combination of the structural variables contribute to improve the understanding of the spatial structure of the forest, and in addition to contributing to the regulation of cutting intensity and ensuring sustainable management.

Lack of knowledge of individual tree growth in species-rich, mixed forest ecosystems impedes their sustainable management. In this study, species-specific models for predicting individual diameter at breast height (dbh) and total tree height (h) growth were developed for 30 tree species growing in mixed and uneven-aged forest stands in Durango, Mexico. Growth models were also developed for all pine, all oaks, and all other species of the genus Arbutus (strawberry trees). A database of 55,158 trees with remeasurements of dbh and h of a 5-year growth period was used to develop the models. The data were collected from 217 stem-mapped plots located in the Sierra Madre Occidental (Mexico). Weighted regression was used to remove heteroscedasticity from the species-specific dbh and h growth models using a power function of the tree size independent variables. The final models developed in the present study to predict dbh and total tree height growth included size variables, site factors, and competition variables in their formulation. The developed models fitted the data well and explained between 98 and 99% and of the observed variation of dbh, and between 77 and 98% of the observed variation of total tree height for the studied species and groups of species. The developed models can be used for estimating the individual dbh and h growth for the analyzed species and can be integrated in decision support tools for management planning in these mixed forest ecosystems This study was supported by the National Forestry Commission (CONAFOR) and the Mexican National Council for Science and Technology (CONACYT) SI

Patients with multirefractory immune thrombocytopenia (ITP) have limited treatment options. Recent data suggest that specific anti-platelet antibodies may cause destruction of platelets by favoring platelet loss of sialic acid. In this multicenter study 35 patients with ITP, including 16 with multirefractory disease, were analyzed for antiplatelet-antibodies, thrombopoietin (TPO) levels, and platelet desialylation. In selected cases, responses to a novel treatment strategy using oseltamivir were tested. We found that antibodies against GPIbα were overrepresented in multirefractory patients compared to responders (n = 19). In contrast to conventional ITP patients, multirefractory patients exhibited a significant increased platelet activation state (granule secretion) and desialylation (RCA-1 binding) (p These findings suggest that desialylation may play a key pathogenic role in some multirefractory ITP patients, and provide diagnostic tools for the identification of such patients. Furthermore, we show that sialidase inhibitor treatment in combination with therapies that help to increase platelet production can induce sustained platelet responses in some patients with anti-GPIbα -mediated thrombocytopenia that have failed previous therapies.

La densidad básica (DB) y poder calorífico superior (PCS) son atributos importantes en la producción de biomasa con fines dendroenergéticos. El objetivo de la presente investigación consistió en determinar la densidad básica de la madera y el poder calorífico superior en vástagos provenientes de tocones de tres cultivos dendroenergéticos. El estudio se realizó en la región del Biobío, Chile, en una plantación de Eucalyptus globulus, E. denticulata y Acacia dealbata con densidades de 5 000, 10 000 y 15 000 árboles por hectárea. Se observaron diferencias para DB de la madera entre especies y E. denticulata registró el nivel más alto en las tres densidades de plantación, con valores entre 0.46 y 0.49 g cm-3. Eucalyptus globulus y A. dealbata mostraron DB similar, con valores entre 0.38 y 0.45 g cm-3. El PCS presentó diferencias entre taxones, en cada tipo de vástago (adventicios y proventicios). Las hojas de vástagos proventicios tuvieron el PCS más alto, con valores de 5 280 kcal kg-1 (22.1 MJ kg-1) en E. globulus; 5 150 kcal kg-1 (21.5 MJ kg-1) en E. denticulata y 4 927 kcal kg-1 (20.6 MJ kg-1) en A. dealbata. En tallos y ramas se observaron niveles de PCS de 4 399 kcal kg-1 (18.4 MJ kg-1) a 4 691 kcal kg-1 (19.6 MJ kg-1). En los vástagos proventicios de E. globulus, E. denticulata y, en menor medida, A. dealbata se registraron valores aceptables para DB y PCS, lo que hace recomendable su uso con fines dendroenergéticos. Se sugieren podas y aclareos para manejar dos vástagos proventicios por tocón y con ello mejorar la DB y el PCS.

Variable-top stem biomass models at the tree level for second growth forests of roble (Nothofagus obliqua), rauli (Nothofagus alpina), and coigue (Nothofagus dombeyi) were fitted by a simultaneous density-integral system, which combines a stem taper model and a wood basic density model. For each model, an autoregressive structure of order 2 and a power equation of residual variance were incorporated to reduce residual autocorrelation and heteroscedasticity, respectively. By using dummy variables in the regression analysis, zonal effects on the parameters in the variable-top stem biomass equations were detected in roble. Consequently, equations for clusters of zones were obtained. These equations presented significant parameters and a high precision in both fitting and validation processes (i.e., CV

We describe a patient with MDS/MPN with ring sideroblasts and thrombocytosis who had deletions of long arm of chromosome 5 (5q-) and chromosome 20 (20q-). Molecular studies showed an exon 9, frame shift mutation in the calreticulin (CALR) gene, and absence of mutations in JAK2, MPL, SETBP1 or SF3B1.Treatment with lenalidomide resulted in durable clinical remission which has lasted 2 years. Keywords: MDS/MPN, Ring sideroblast, Thrombocytosis, 5q, Lenalidomide

Essentials Vitamin K-dependent coagulant factor deficiency (VKCFD) is a rare autosomal recessive disorder. We describe a case of inherited VKCFD due to uniparental disomy. The homozygous mutation caused the absence of GGCX isoform 1 and overexpression of Δ2GGCX. Hepatic and non-hepatic vitamin K-dependent proteins must be assayed to monitor VKCFD treatment. Summary: Background Inherited deficiency of all vitamin K-dependent coagulant factors (VKCFD) is a rare autosomal recessive disorder caused by mutations in the γ-glutamyl carboxylase gene (GGCX) or the vitamin K epoxide reductase gene (VKORC1), with great heterogeneity in terms of both clinical presentation and response to treatment. Objective To characterize the molecular basis of VKCFD in a Spanish family. Methods and Results Sequencing of candidate genes, comparative genomic hybridization and massive sequencing identified a new mechanism causing VKCFD in the proband. Uniparental disomy (UPD) of chromosome 2 caused homozygosity of a mutation (c.44-1G>A) resulting in aberrant GGCX splicing. This change contributed to absent expression of the mRNA coding for the full-length protein, and to four-fold overexpression of the smaller mRNA isoform lacking exon 2 (Δ2GGCX). Δ2GGCX might be responsible for two unexpected clinical observations in the patient: (i) increased plasma osteocalcin levels following vitamin K supplementation; and (ii) a mild non-bleeding phenotype. Conclusions Our study identifies a new autosomal disease, VKCFD1, caused by UPD. These data suggest that the Δ2GGCX isoform may retain enzymatic activity, and strongly encourage the evaluation of both hepatic and non-hepatic vitamin K-dependent proteins to assess differing responses to vitamin K supplementation in VKCFD patients., This work was supported by PI15/00079 and 19873/GERM/15 (Fundacion Seneca). M. E. de la Morena-Barrio holds a postdoctoral contract from MEC FPDI-2013-17273.

Background Dissimilarity in community composition is one of the most fundamental and conspicuous features by which different forest ecosystems may be distinguished. Traditional estimates of community dissimilarity are based on differences in species incidence or abundance (e.g. the Jaccard, Sørensen, and Bray-Curtis dissimilarity indices). However, community dissimilarity is not only affected by differences in species incidence or abundance, but also by biological heterogeneities among species. Methods The objective of this study is to present a new measure of dissimilarity involving the biological heterogeneity among species. The “discriminating Avalanche” introduced in this study, is based on the taxonomic dissimilarity between tree species. The application is demonstrated using observations from five stem-mapped forest plots in China and Mexico. We compared three traditional community dissimilarity indices (Jaccard, Sørensen, and Bray-Curtis) with the “discriminating Avalanche” index, which incorporates information, not only about species frequencies, but also about their taxonomic hierarchies. Results Different patterns emerged for different measures of community dissimilarity. Compared with the traditional approaches, the discriminating Avalanche values showed a more realistic estimate of community dissimilarities, indicating a greater similarity among communities when species were closely related. Conclusions Traditional approaches for assessing community dissimilarity disregard the taxonomic hierarchy. In the traditional analysis, the dissimilarity between Pinus cooperi and Pinus durangensis would be the same as the dissimilarity between P. cooperi and Arbutus arizonica. The dissimilarity Avalanche dissimilarity between P. cooperi and P. durangensis is considerably lower than the dissimilarity between P. cooperi and A. arizonica, because the taxonomic hierarchies are incorporated. Therefore, the discriminating Avalanche is a more realistic measure of community dissimilarity. This main result of our study may contribute to improved characterization of community dissimilarities. Open-Access-Publikationsfonds 2019

Infection by human papillomavirus (HPV) alters the microenvironment of keratinocytes as a mechanism to evade the immune system. A-to-I editing by ADAR1 has been reported to regulate innate immunity in response to viral infections. Here, we evaluated the role of ADAR1 in HPV infection in vitro and in vivo. Innate immune activation was characterized in human keratinocyte cell lines constitutively infected or not with HPV. ADAR1 knockdown induced an innate immune response through enhanced expression of RIG-I-like receptors (RLR) signaling cascade, over-production of type-I IFNs and pro-inflammatory cytokines. ADAR1 knockdown enhanced expression of HPV proteins, a process dependent on innate immune function as no A-to-I editing could be identified in HPV transcripts. A genetic association study was performed in a cohort of HPV/HIV infected individuals followed for a median of 6 years (range 0.1–24). We identified the low frequency haplotype AACCAT significantly associated with recurrent HPV dysplasia, suggesting a role of ADAR1 in the outcome of HPV infection in HIV+ individuals. In summary, our results suggest that ADAR1-mediated innate immune activation may influence HPV disease outcome, therefore indicating that modification of innate immune effectors regulated by ADAR1 could be a therapeutic strategy against HPV infection.

Ground contact speeds up timber decay because of the large number of microorganisms in soil. This study, we assessed the natural durability of seven tropical species using the European standard EN-807 (2001). We embedded samples of Dalbergia granadillo, Cordia elaeagnoides, Swietenia humillis, Tabebuia donell-smithii, Hura polyandra, Enterolobium cyclocarpum and Tabebuia rosea and temperate species Fagus sylvatica (as a control) in sandy, clay-sandy-loam and clay-loam for 8, 16, 24 and 32 weeks. We evaluated durability of the samples by determining the mass loss and modulus of elasticity (MOE) loss. The results varied significantly (p < 0,001) depending on timber species and soil type considered. The D. granadillo and C. elaeagnoides were the most durable, with mass losses of 4,5%; 6,5% and MOE losses of 4,5%; 20,5%; respectively. F. sylvatica, T. rosea and E. cyclocarpum samples were the least durable, with mass losses of 22,3-25% and MOE losses of 35,8-59,8% respectively. Decay was most aggressive in sandy-clay-loam soil followed by the clay-loam soil and finally the sandy soil.

Bleeding is a relatively common complication in patients with multiple myeloma. Different factors have been involved, such as heparin-like anticoagulants, although the underlying mechanism remains obscure. The identification of a patient with a quiescent multiple myeloma IgG-γ that suffered a

A crown profile model for Pinus cooperi Blanco in UMAFOR 1008 (El Salto, Pueblo Nuevo, Durango) was developed from data corresponding to 92 sampled trees. Trees with well-formed crowns were selected from stands varying in age, density and site quality. Diameter at breast height, total height, crown width, crown length, and crown profile were measured in each tree. To predict the crown profile, basic geometric shapes and several mathematic models were evaluated. The model developed by Hann (1999) best described the experimental data of the total crown, light crown, and shaded crown, accounting for over 92 % of the observed variability. Se desarrolló un modelo de perfil de copa para Pinus cooperi Blanco a partir de 92 árboles en la UMAFOR 1008 (Región El Salto, Pueblo Nuevo, Durango). Se seleccionaron individuos con una copa bien conformada y de diferente edad, densidad y calidad de estación. En cada uno de los individuos se midieron las variables diámetro normal, altura total, diámetro, longitud y perfil de copa. Tanto formas geométricas sencillas como algunos modelos matemáticos se analizaron para predecir el perfil de la copa. El mejor modelo para describir el perfil de copa de P. cooperi fue el de Hann (1999), ya que tuvo mejor ajuste para la copa entera, copa de luz y copa de sombra, explicando más de 92 % de la variabilidad de los datos. SI

With Ernst Assmann’s appointment to the chair of Forest Yield Science in Munich in 1951, he assumed responsibility for the maintenance of the extensive network of growth-and-yield plots of the Bavarian Forest Research Institute. This network, with some plots having been remeasured since 1870, proved to be a rich source of observations, and constituted the empirical basis for Assmann’s fundamental theories in production ecology. Realizing the strategic value of long-term field observations, scientists are using (a) designed experiments and (b) observational studies to study forest structure and dynamics. This contribution is an attempt to clarify fundamental differences, and to present examples, of these two approaches. We present recent developments regarding the installation of Designed Experiments and show that rigorous experimental design, usually found in planted forests and based on very specific manipulations, that are normally not found in the natural environment is required to address a particular hypothesis that cannot be tested by merely using available observations. We also present examples of new Forest Observational Networks established in China, India, Africa and America. These alternative research infrastructures are especially suitable for the study of natural forests that exhibit a high diversity of tree species with varying size and age structures. Our conclusion is that Forest Observational Studies are emerging as an important alternative to Designed Experiments because they provide a vast amount of information about complex natural forest communities rather quickly. However, long-term commitment is essential to ensure a steady flow of observations about forest dynamics. Manipulated experiments and observational studies can be complementary, but the optimum use of both installations requires careful planning and coordination.

El objetivo del presente trabajo fue determinar el depósito y la tasa de descomposición de hojarasca de Pinus cooperi en parcelas bajo diferentes intensidades de aclareos (tratamientos) (testigo; T1: Aclareo ligero; T2: Moderado; T3: Fuerte; T4: Severo; T5: Porvenir) en el ejido La Ciudad de Pueblo Nuevo, Durango. Después de un año de observación, la máxima acumulación de hojarasca se registró en el tratamiento Testigo (4.90 Mg ha-1 año-1), seguido por T2 (3.76 Mg·ha-1·año-1), T1 (3.65 Mg·ha-1·año-1), T4 (3.25 Mg·ha-1·año-1) y T3 (3.04 Mg·ha-1·año-1). El menor aporte anual de hojarasca se registró en el T5 (2.58 Mg ha-1 año-1). La tasa de descomposición (k) de la hojarasca se determinó a partir del modelo exponencial de Olson. Las tasas diarias de descomposición fueron mayores durante los primeros 150 días de incubación que en los 210 días subsiguientes. En ambos periodos hubo diferencias significativas entre los tratamientos. Después de 360 días de incubación, la mayor descomposición de hojarasca ocurrió en T3 (42.3 %), independientemente de la densidad residual de las parcelas; en el resto de los tratamientos, la descomposición varió de 30.2 (T1) a 37.1 %(T5). Aun cuando en T3 fue significativamente más rápida que en los demás tratamientos, bajo las condiciones de microclima que ofrecen estos tipos de aclareos, no se detectaron diferencias entre las tasas de descomposición para las cinco condiciones evaluadas en este estudio.

El objetivo del trabajo consistió en el desarrollo de ecuaciones alométricas para estimar la biomasa aérea por fracciones de grosor de la regeneración de Arbutus arizonica, Juniperus deppeana, Quercus sideroxyla y Pinus cooperi en la Unidad de Manejo Forestal (Umafor 1008) en el estado de Durango. Se utilizaron datos provenientes de 114 individuos (25, 29, 30 y 30, respectivamente), colectados mediante un muestreo destructivo para ajustar los modelos. La aditividad de las ecuaciones de estimación de biomasa se aseguró mediante el ajuste simultáneo de todas las ecuaciones, con el procedimiento estadístico denominado 3SLS (Three-Stage Least Squares). Los modelos desarrollados permiten estimar la biomasa en peso seco de los componentes, peso total, hojas, ramillas (< 0.5 cm), ramas finas (0.51 – 2.5 cm), ramas gruesas y tronco (> 2.51 cm). Las ecuaciones alométricas con mejor ajuste correspondieron al peso total, con valores de coeficiente de determinación ajustado de 0.97, 0.94, 0.95 y 0.97 para Arbutus, Juniperus, Quercus y Pinus cooperi, respectivamente. En general las ecuaciones mostraron un ajuste satisfactorio en cada una de las fracciones; con ellas se podrán hacer estimaciones no destructivas de la biomasa por categoría de grosor de la regeneración de las cuatro especies estudiadas, lo que mejorará las predicciones de biomasa y almacén de carbono por fracciones en los bosques con presencia de los cuatro taxa estudiados.

Motivation Translation is a key biological process controlled in eukaryotes by the initiation AUG codon. Variations affecting this codon may have pathological consequences by disturbing the correct initiation of translation. Unfortunately, there is no systematic study describing these variations in the human genome. Moreover, we aimed to develop new tools for in silico prediction of the pathogenicity of gene variations affecting AUG codons, because to date, these gene defects have been wrongly classified as missense. Results Whole-exome analysis revealed the mean of 12 gene variations per person affecting initiation codons, mostly with high (>0.01) minor allele frequency (MAF). Moreover, analysis of Ensembl data (December 2017) revealed 11 261 genetic variations affecting the initiation AUG codon of 7205 genes. Most of these variations (99.5%) have low or unknown MAF, probably reflecting deleterious consequences. Only 62 variations had high MAF. Genetic variations with high MAF had closer alternative AUG downstream codons than did those with low MAF. Besides, the high-MAF group better maintained both the signal peptide and reading frame. These differentiating elements could help to determine the pathogenicity of this kind of variation. Availability and implementation Data and scripts in Perl and R are freely available at https://github.com/fanavarro/hemodonacion. Supplementary information Supplementary data are available at Bioinformatics online.

In this paper the effect of competition on individual tree diameter growth of Pinus durangensis was analyzed. Trees were growing in mixed and uneven-aged stands in Durango, Mexico. The data used in the study were obtained from two forest inventories performed in 2009 and 2014 in 16 permanent sampling plots for forest and soil research (SPIFyS) of 2 500 m2 in size. Pinus durangensis was the dominant species within the sites, covering 39.44 % of the importance value, and it is growing with other 18 tree species. 14 distance-independent and 11 distance-dependent competition indices were used to evaluate the effect of competition. 11 competitor selection methods were tested in combination with the selected distance-dependent indices. Distance-independent competition indices showed slightly better results than distance-dependent indices for predicting diameter at breast height growth for the studied tree species. The distance-independent competition index derived from the ratio between of the basal area of the reference tree and the basal area per hectare best described the effect of the competition, and therefore, it is recommended for its possible addition within further models to predict the breast height diameter growth for the tree species analyzed in this study.

International audience; AbstractKey messageMore accurate diameter at breast height (dbh)-growth models are needed for developing management tools for mixed-species forests in Mexico. Individual distance-dependent dbh growth models that quantify local neighborhood effects have been developed for four species groups in such forests. The performance of the models is improved by distinguishing between inter- and intraspecific group competitions.ContextThe management of mixed-species forests in the northwest of Durango, Mexico, is mainly based on the selection method. Understanding the interspecific and intraspecific competition is critical to developing management tools for such mixed-species forests.AimsAn individual-based distance-dependent modeling approach was used to model the growth of dbh and to evaluate neighborhood effects for four species groups in Mexican mixed-species stands.MethodsTwenty-two species were classified into four groups: Pinus (seven species), other conifers (three species), other broadleaves (four species), and Quercus (eight species). Four methods were used to select neighboring trees and 12 competition indices (CIs) were calculated. Comparisons of the neighboring trees selection methods and CIs and tests of assumptions about neighborhood effects were conducted.ResultsIntra-species-group competition significantly reduced diameter growth for all species groups, except for the Quercus group. The Pinus, other conifers, and Quercus groups had significant and negative neighborhood effects on the other broadleaves species group, and not vice versa. The Quercus group also had negative neighborhood effect on the Pinus and other conifers species groups, and not vice versa. The Pinus and other conifers species groups had negative neighborhood effects on each other. All fitted age-independent dbh growth models showed a good of fit to the data (adjusted coefficient of determination larger than 0.977).ConclusionThe growth models can be used to predict dbh growth for species groups and competition in mixed-species stand from Durango, Mexico.

Quantitative and qualitative composition of the foliar phenolic compounds were investigated in 81 individual specimens of several white oak species (Quercus spp.). The trees were growing in twelve locations in Durango, Mexico. The phenol profiles were determined by HPLC-DAD and a Folin-Ciocateu procedure. The results revealed that: (i) the foliar phenol profiles of all species analysed were complex and formed by 6 to 30 compounds, (ii) the flavonols mostly quercetin glycoside, isorhamnetin glycoside, kaempferol glycoside and phenolic acids were the main identified compounds, (iii) there was a high intra and inter-specific variability in the foliar phenol profiles both at the quantitative and qualitative levels, and (iv) the foliar phenol profiles indicated a slight species-specific tendency for phenols to be accumulated, although this was not clearly distinguished. Significant differences (P < 0.05) in the content and composition of the foliar flavonoids between species were observed due to the large environmental and soil conditions variability between localities.

Three irrigation periods (every 48, 96 and 192 hours) were evaluated with the purpose of improving the preconditioning Pinus engelmannii Carr. seedlings in nursery. Eight months old seedlings were evaluated for 40 days. The study was conducted under greenhouse conditions at the nursery of the Experimental Station Valle del Guadiana of INIFAP. The data were analyzed with a permutations test. The results show that irrigation every 48 h caused the best effects in height (7.70 cm), diameter (4.38 mm), total biomass (6.59 g) and Dickson’s quality index (0.55). In contrast, water stress caused by treatment with irrigation every 192 h (-1.22 MPa) limited the growth of seedlings; however, the lignification index (26.63) was significantly better (P = 0.0001) with this frequency of irrigation. Despite having significant differences (P = 0.0001) in the hydric potential and morphological variables, there was not sufficient evidence to define an absolutely superior treatment to improve the preconditioning of seedlings in the nursery. Therefore, it is advisable to evaluate these treatments for a longer time; moreover, it is suggested to evaluate the same treatments in the plantation field.

// Jose Navarro-Fernandez 1, * , Maria Eugenia de la Morena-Barrio 1, * , Emma Martinez-Alonso 2 , Ingunn Dybedal 3 , Mara Toderici 1 , Nataliya Bohdan 1 , Antonia Minano 1 , Ketil Heimdal 4 , Ulrich Abildgaard 3 , Jose Angel Martinez-Menarguez 2 , Javier Corral 1 and Vicente Vicente 1 1 Servicio de Hematologia y Oncologia Medica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonacion, Universidad de Murcia, IMIB-Arrixaca, CIBERER, Murcia, Spain 2 Department of Cellular Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain 3 Department of Haematology, Oslo University Hospital, Oslo, Norway 4 Department of Medical Genetics, Oslo University Hospital, Oslo, Norway * These authors have contributed equally to this work Correspondence to: Javier Corral, email: javier.corral@carm.es Keywords: antithrombin; thrombosis; initiation codon; translation Received: November 30, 2017 Accepted: July 31, 2018 Published: September 04, 2018 ABSTRACT Nature is always the best inspiration for basic research. A family with severe thrombosis and antithrombin deficiency, the strongest anticoagulant, carried a new mutation affecting the translation-start codon of SERPINC1 , the gene encoding antithrombin. Expression of this variant in a eukaryotic cell system produced three different antithrombins. Two downstream methionines were used as alternative initiation codons, generating highly expressed small aglycosylated antithrombins with cytoplasmic localization. Wild-type antithrombin was generated by the use of the mutated AUU as initiation codon. Actually, any codon except for the three stop codons might be used to initiate translation in this strong Kozak context. We show unexpected consequences of natural mutations affecting translation-start codons. Downstream alternative initiation AUG codons may be used when the start codon is mutated, generating smaller molecules with potential different cell localization, biochemical features and unexplored consequences. Additionally, our data further support the use of other codons apart from AUG for initiation of translation in eukaryotes.

Introduction Factor XI (FXI) deficiency is a rare disorder with molecular heterogeneity in Caucasians but relatively frequent and molecularly homogeneous in certain populations. Aim To characterize FXI deficiency in a Spanish town of 60 000 inhabitants. Methods A total of 324 764 APTT tests were screened during 20 years. FXI was evaluated by FXI:C and by Western blot. Genetic analysis of F11 was performed by sequencing, multiplex ligation-dependent probe amplification and genotyping. Results Our study identified 46 unrelated cases and 170 relatives with FXI deficiency carrying 12 different genetic defects. p.Cys56Arg, described as founder mutation in the French-Basque population, was identified in 109 subjects from 24 unrelated families. This mutation was also identified in 2% of the general population. p.Cys416Tyr, c.1693G>A and p.Pro538Leu were identified in 7, 6 and 2 unrelated families, respectively. NGS analysis of the whole F11 gene revealed a common haplotype for each of the four recurrent mutations, suggesting a founder effect. The analysis of plasma FXI of four p.Pro538Leu homozygous carriers revealed that this variant was not activated by FXIIa. We identified four mutations previously described in other Caucasian subjects with FXI deficiency (p.Lys536Asn; p.Thr322Ile, p.Arg268Cys and c.325G>A) and four new gene defects: p.(Cys599Tyr) potentially causing a functional deficiency, p.(Ile426Thr), p.(Ile592Thr) and the first worldwide duplication of 1653 bp involving exons 8 and 9. Bleeding was rare and mild. Conclusions Our population-cohort study supplies new evidences that FXI deficiency in Caucasians is more common than previously thought and confirmed the wide underlying genetic heterogeneity, caused by both recurrent and sporadic mutations.

An in-depth focused study of specific cases of patients with recurrent thrombosis may help to identify novel circumstances, genetic and acquired factors contributing to the development of this disorder. The aim of this study was to carry out a detailed and sequential analysis of samples from a patient suffering from early and recurrent venous and arterial thrombosis. We performed thrombophilic tests, biochemical, functional, genetic and glycomic analysis of antithrombin and other plasma proteins. The patient carried a new type I antithrombin mutation (p.Ile218del), whose structural relevance was verified in a recombinant model. Experiments with N-glycosidase F and neuraminidase suggested a nearly full desialylation of plasma proteins, which was confirmed by mass spectrometry analysis of transferrin glycoforms. However, partial desialylation and normal patterns were detected in samples collected at other time-points. Desialylation was noticeable after arterial events and was associated with low antithrombin activity, reduced platelet count and glomerular filtration rate. This is the first description of a global and transient desialylation of plasma proteins associated with thrombosis. The decrease in the strong electronegative charge of terminal glycans may modulate hemostatic protein-protein interactions, which in combination with a strong prothrombotic situation, such as antithrombin deficiency, could increase the risk of thrombosis.

Accurate quantification of branch volume in trees is important for sustainable forest management, especially as these fractions are increasingly used for bioenergy, and for precise forest CO2 quantification. Whereas a large focus has been placed on the compatible estimation of tree taper and bole volume with and without bark, little effort has been made to develop models that allow a simultaneous prediction of these variables together with tree branch volume. In this study, 595 Pinus cooperi trees and 700 Pinus durangensis trees were sampled in pine-oak forests in the Sierra Madre Occidental, Mexico. A compatible system for predicting two segmented taper functions, over and under bark; the corresponding merchantable volumes; coarse branch volume and whole-tree volume was fitted using a modified continuous autoregressive structure to account for autocorrelation. The proposed compatible equations explained more than 97% of the observed variability in diameter over and under bark, volume over and under bark, and total tree volume and more than 64% of the observed variability in branch volume in both species. The method described can theoretically be replicated for any tree species, thus providing a better understanding of the patterns of volume distribution by components, potentially improving carbon accounting system and forest bioenergy planning. SI

Aim of study: To propose a new approach to defining rotation ages on the basis of productive and technological aspects and to present an example of application of the methodology to natural Pinus sylvestris stands in relation to silvicultural treatment (light or heavy thinning) and site index. Area of study: Central Spain. Material and methods: We assumed that the price per m3 of logwood suitable for veneer is four times higher than logwood not apt for veneer. Considering the yield distribution for different technological and commercial classes, a model of diameter distributions and yield tables, the variation in an average price index for different age classes, site indexes and silvicultural treatments was calculated. The age at which the price index rises by less than 3%, the proportion of trees with d.b.h. higher than 40 cm, and other aspects such as the possible presence of fungal decay in old-growth stands were also taken into account to establish three criteria for defining rotation ages. Main results: The proposed methodology generates a wide range of rotation ages between 100 and 140 years for lightly thinned stands, and between 90 and 140 years for heavily thinned stands, depending on the site index. Research highlights: The proposed approach is based on technological and productive criteria, with the limitations imposed by sanitary risks. The methodology can be applied to generate rotation ages in relation to different site indexes and silvicultural treatments, provided that the timber market prices and the yield distribution for different technological and commercial classes are known, and that a model of diameter distributions and yield tables are available. SI

INTRODUCTION Inherited deficiencies of natural anticoagulants such as antithrombin (AT; gene: SERPINC1), protein C (PC; PROC), and protein S (PS; PROS1), with the prevalence in the general European population of 0.02% to 0.17%, 0.2% to 0.3%, and 0.5%, respectively, are associated with increased risk of thromboembolic events. Only a few case reports of Polish deficient patients with known causal mutations have been published so far. OBJECTIVES The aim of the study was to characterize the frequency of SERPINC1, PROC, and PROS1 mutations and their thromboembolic manifestations in patients with AT, PC, or PS deficiencies, inhabiting southern Poland. PATIENTS AND METHODS Ninety unrelated patients (mean [SD] age, 40.1 [13.2] years) with AT (n = 35), PC (n = 28), or PS (n = 27) deficiencies, with a history of venous 73 (81%) or arterial 17 (19%) thromboembolism, were screened for mutations using the Sanger sequencing or multiplex ligation‑dependent probe amplification. RESULTS Twenty mutations (29%) described here were new, mostly in the SERPINC1 and PROC genes. Missense mutations accounted for 84% of all mutations in the PROC gene and approximately 50% of those in the SERPINC1 and PROS1 genes. In all 3 genes, the ratio of nonsense and splice-site mutations was 8% to 31% and 8% to 23%, respectively. The mutation detection rate was 90% for AT or PC when anticoagulant activity was below 70%, while for the PROS1 gene, the rate reached 80% at the free PS levels below 40%. CONCLUSIONS To our knowledge, this is the largest cohort of Polish patients deficient in natural anticoagulants and evaluated for the causal genetic background. Several new Polish detrimental mutations were detected, mostly in AT- and PC‑deficient patients.

Introduction: Estimating the volume of individual trees is an important aspect in dendrometry and in the conducting of forest inventories. Objective: Significant differences were evaluated in additive equation systems for estimating the total volume of individual trees in nine species of the genus Pinus (P. cooperi, P.durangensis, P. arizonica, P. leiophylla, P. teocote, P. engelmannii, P. lumholtzii, P.strobiformisand P. herrerae), and three of the genus Quercus (Q. sideroxyla, Q. durifoliaand Q. rugosa), and among regional forest management units (UMAFOR) when dealing with the same species. Materials and methods: To evaluate whether equation systems are different among tree species of the same genus and among the UMAFORs for the same species, two complementary statistical analyzes were used based on the fitting of a reduced and a full equation system: the F test of nonlinear extra sum of squares method, and the parameter significance analysis. Results and discussion: For most of the species studied, equation systems are significantly different. The need to use regional models in 10 of the 12 tree species, except for P. strobiformis and Q. rugosa, is also reported. Conclusion: The use of a state model for P. strobiformis and Q. rugosa is recommended. Introducción: La estimación del volumen de árboles individuales es un aspecto relevante en la dendrometría y en la realización de inventarios forestales. Objetivo: Se evaluaron diferencias significativas en sistemas de ecuaciones aditivas para la estimación de volumen total de árboles individuales en nueve especies de Pinus (P. cooperi, P. durangensis, P. arizonica, P. leiophylla, P. teocote, P. engelmannii, P. lumholtzii, P. strobiformis y P. herrerae), y tres de Quercus (Q. sideroxyla, Q. durifolia y Q. rugosa), y entre unidades de manejo forestal regional (UMAFOR) cuando se trata de una misma especie. Materiales y métodos: Para evaluar si el sistema de ecuaciones difiere entre especies de un mismo género y entre las UMAFOR para una misma especie, se utilizaron dos análisis estadísticos complementarios basados en el ajuste de un sistema reducido y un sistema completo de ecuaciones: la prueba F asociada al método de la suma adicional de cuadrados no lineales y el análisis de significancia de los parámetros. Resultados y discusión: Para la mayoría de las especies estudiadas, los sistemas de ecuaciones son significativamente diferentes. Se reporta la necesidad de utilizar modelos regionales en 10 de las 12 especies, exceptuando a P. strobiformis y Q. rugosa. Conclusiones: Se recomienda el empleo de un modelo estatal para P. strobiformis y Q. rugosa. We thank the Program Fomento a la Organización Social,Planeación y Desarrollo Regional Forestal (PROFOS) of CONAFOR for funding the collection of the data used in this study SI

Summary Background The characterization of natural mutants identified in patients with antithrombin deficiency has helped to identify functional domains or regions of this key anticoagulant and the mechanisms involved in the deficiency, as well as to define the clinical prognosis. Recently, we described an abnormal glycosylation in a pleiotropic mutant (K241E) that explained the impaired heparin affinity and the mild risk of thrombosis in carriers. Objectives To evaluate the effects of different natural pleiotropic mutations on the glycosylation of antithrombin and their functional effects. Methods Five pleiotropic mutations identified in patients with antithrombin deficiency and located at each one of the strands of the C-sheet were selected (K241E, M251I, M315K, F402L, and P429L). Recombinant mutants were generated and purified. Glycoform heterogeneity and conformational sensitivity were studied with electrophoresis, proteomic analysis, and glycomic analysis. Heparin affinity was evaluated from intrinsic fluorescence. Reactivity assays with factor Xa, thrombin and neutrophil elastase in the presence or absence of heparin were also performed. Results and Conclusions Pleiotropic mutants, except for that with the M315K mutation, which affects a non-exposed residue, showed two glycoforms. Variant 1, with abnormal glycosylation, had reduced heparin affinity and severely affected reactivity with the target proteases. In contrast, variant 2, with similar electrophoretic mobility and heparin affinity to wild-type antithrombin, had impaired inhibitory activity that was partially compensated for by activation with heparin. Our results suggest the C-sheet of antithrombin as a new region that is relevant for proper maturation of the N-glycans. Therefore, pleiotropic mutations lead to glycosylation defects that are responsible for the reduced heparin affinity.

CSN1S2 gene encodes the αS2-casein, one of the phosphoproteins (αS1, β, αS2 and κ) secreted in ruminants milk in form of stable calcium–phosphate micelles. CSN1S2⁎B variant contains the amino acid substitutions p.Asp75Tyr and p.Ile105Val in the mature protein. Recently, we have shown that two adjacent SNPs, [FN_601350: g.153G>T and 155C>T], located at exon 10, are causers of the p.Asp75Tyr substitution, while the non-synonymous mutation SNP [FN_601350: g.504A>G], in exon 11, led to codon exchange of p.Ile105Val. PCR-RFLP and RT-PCR analyses were used to detect and characterize the single nucleotide polymorphisms involved in the B variant of the CSN1S2 gene and to assess their effects on milk yield and composition traits. Four hundred and thirty samples from different breeds (Berrinchon du cher, Castellana, Ile de France and Merino) were analyzed and population genetic parameters were estimated for each locus and breed. Both polymorphic sites of the SNPs g.[153G>T and 155C>T] are conserved across analyzed breeds. Haplotype allele frequencies from the SNPs g.[153G>T and 155C>T]—GC, GT, TC and TT—varied among the breeds, being GC the most frequent allele in all populations (>0.5). Allele G from SNP g.504A>G had the minor allele frequency in all breeds analyzed (ranged from 0.225 to 0.333). The value of genetic differentiation (FST=0.0419) across breeds and loci indicates that there was no genetic divergence among the analyzed breeds. The haplotype frequencies, the deduced amino acid haplotypes and the occurrence of linkage disequilibrium were estimated in a large population (377 samples) of Merino sheep breed. The eight possible haplotypes of these two loci were identified, and substantial linkage disequilibrium was found. GCA was the haplotype most frequent (>70%) and Asp75–Ile105 the most frequent aminoacid haplotype (0.713). Recombinants haplotypes were observed in low frequencies (≤0.1). Association study between the ovine CSN1S2⁎B polymorphisms and the milk traits were estimated in 669 lactations from 218 Merino ewes. The CSN1S2 p.75 and CSN1S2 p.105 polymorphisms affected the non-fat solids and lactose percentages in milk, respectively. The CSN1S2 Tyr75Tyr ewes had the highest levels of non fat solids and the ewes carrying CSN1S2 Val105Val genotype had the smallest lactose percentage. Similar effects of the single markers have been observed for homozygous Tyr75–Val105 ewes on lactose percentage. This work provides the basis to study in further sheep breeds the CSN1S2⁎B polymorphisms and their effects on milk traits.

Antithrombin is a crucial anticoagulant serpin whose even moderate deficiency significantly increases the risk of thrombosis. Most cases with antithrombin deficiency carried genetic defects affecting exons or flanking regions of SERPINC1.We aimed to identify regulatory mutations inSERPINC1 through sequencing the promoter, intron 1 and 2 of this gene in 23 patients with antithrombin deficiency but without known genetic defects. Three cases with moderate antithrombin deficiency (63-78%) carried potential regulatory mutations. One located 200 bp before the initiation ATG and two in intron 1. These mutations disrupted two out of five potential vitamin D receptor elements (VDRE) identified in SERPINC1 with different software. One genetic defect, c.42-1060_-1057dupTTGA, was a new low prevalent polymorphism (MAF: 0.01) with functional consequences on plasma antithrombin levels. The relevance of the vitamin D pathway on the regulation of SERPINC1 was confirmed in a cell model. Incubation of HepG2 with paricalcitol, a vitamin D analog, increased dose-dependently the levels of SERPINC1transcripts and antithrombin released to the conditioned medium. This study shows further evidence of the transcriptional regulation of SERPINC1 by vitamin D and first describes the functional and pathological relevance of mutations affecting VDRE of this gene. Our study opens new perspectives in the search of new genetic defects involved in antithrombin deficiency and the risk of thrombosis as well as in the design of new antithrombotic treatments.

Genomic medicine pursues to develop methods for improving early diagnosis processes, the efficiency of treatments and facilitating the discovery of new therapies, and mainly searches for associations between the genotype of individuals and their phenotypical features. The huge genomic variability is a major difficulty for developing effective computational methods, since the correlation of a locus and a phenotype does not necessarily mean causality. Hence, methods for genome-based diagnosis need to take into account the complexity of the genomic background and the biological networks involved in the manifestation of phenotypes and disorders.

SummaryAntithrombin is the main endogenous anticoagulant. Impaired function or deficiency of this molecule significantly increases the risk of thrombosis. We studied the genetic variability of SERPINC1, the gene encoding antithrombin, to identify mutations affecting regulatory regions with functional effect on its levels. We sequenced 15,375 bp of this gene, including the potential promoter region, in three groups of subjects: five healthy subjects with antithrombin levels in the lowest (75%) and highest (115%) ranges of our population, 14 patients with venous thrombosis and a moderate antithrombin deficiency as the single thrombophilic defect, and two families with type I antithrombin deficiency who had neither mutations affecting exons or flanking regions, nor gross gene deletions. Our study confirmed the low genetic variability of SERPINC1, particularly in the coding region, and its minor influence in the heterogeneity of antithrombin levels. Interestingly, in one family, we identified a g.2143 C>G transversion, located 170 bp upstream from the translation initiation codon. This mutation affected one of the four regions located in the minimal promoter that have potential regulatory activity according to previous DNase footprinting protection assays. Genotype-phenotype analysis in the affected family and reporter analysis in different hepatic cell lines demonstrated that this mutation significantly impaired, although it did not abolish, the downstream transcription. Therefore, this is the first mutation affecting a regulatory region of the SERPINC1 gene associated with antithrombin deficiency. Our results strongly sustain the inclusion of the promoter region of SERPINC1 in the molecular analysis of patients with antithrombin deficiency.