Plant triterpenoid saponins function as susceptibility factors to promote the pathogenicity of Botrytis cinerea.

The gray mold fungus Botrytis cinerea is a necrotrophic pathogen that causes diseases in hundreds of plant species, including high-value crops. Its polyxenous nature and pathogenic success are due to its ability to perceive host signals in its favor. In this study, we found that laticifer cells of Euphorbia lathyris are a source of susceptibility factors required by B. cinerea to cause disease. Consequently, poor-in-latex (pil) mutants, which lack laticifer cells, show full resistance to this pathogen, whereas lot-of-latex mutants, which produce more laticifer cells, are hypersusceptible. These S factors are triterpenoid saponins, which are widely distributed natural products of vast structural diversity. The downregulation of laticifer-specific oxydosqualene cyclase genes, which encode the first committed step enzymes for triterpene and, therefore, saponin biosynthesis, conferred disease resistance to B. cinerea. Likewise, the Medicago truncatula lha-1 mutant, compromised in triterpenoid saponin biosynthesis, showed enhanced resistance. Interestingly, the application of different purified triterpenoid saponins pharmacologically complemented the disease-resistant phenotype of pil and hla-1 mutants and enhanced disease susceptibility in different plant species. We found that triterpenoid saponins function as plant cues that signal transcriptional reprogramming in B. cinerea, leading to a change in its growth habit and infection strategy, culminating in the abundant formation of infection cushions, the multicellular appressoria apparatus dedicated to plant penetration and biomass destruction in B. cinerea. Taken together, these results provide an explanation for how plant triterpenoid saponins function as disease susceptibility factors to promote B. cinerea pathogenicity.

Risk factors for intraoperative hypertensive crisis in patients with pheochromocytomas and sympathetic paragangliomas.

PURPOSE: To identify presurgical and surgical risk factors for intraoperative hypertensive crisis in patients with pheochromocytomas and sympathetic paragangliomas (PGLs) (PPGLs). METHODS: Retrospective multicenter cohort study of patients with PPGLs from 18 tertiary hospitals. Intraoperative hypertensive crisis was defined as systolic blood pressure (SBP) greater than 200 mmHg lasting more than 1 min and postoperative hypertensive crisis as SBP greater than 180 mmHg or diastolic blood pressure (DBP) greater than 110 mmHg. RESULTS: A total of 296 surgeries were included. Alpha presurgical blockade was employed in 93.2% of the cases and beta-adrenergic in 53.4%. Hypertensive crisis occurred in 20.3% ( n  = 60) of the surgeries: intraoperative crisis in 56 and postoperative crisis in 6 cases (2 cases had both types of crises). We identified as risk factors of intraoperative hypertensive crisis, absence of presurgical glucocorticoid therapy (odds ratio [OR] 3.48; 95% confidence interval [CI] 1.19-10.12) higher presurgical SBP (OR 1.22 per each 10 mmHg, 95% CI 1.03-1.45), a larger tumor size (OR 1.09 per each 10 mm, 95% CI 1.00-1.19) and absence of oral sodium repletion (OR 2.59, 95% CI 1.25-5.35). Patients with hypertensive crisis had a higher rate of intraoperative bleeding ( P  < 0.001), of intraoperative hemodynamic instability ( P  < 0.001) and of intraoperative hypotensive episodes ( P  < 0.001) than those without hypertensive crisis. CONCLUSION: Intraoperative hypertensive crisis occurs in up to 20% of the PPGL resections. Patients not pretreated with glucocorticoid therapy before surgery, with larger tumors and higher presurgical SBP and who do not receive oral sodium repletion have a higher risk for developing hypertensive crisis during and after PPGL surgery.

Local recurrence and metastatic disease in pheochromocytomas and sympathetic paragangliomas.

Purpose: To evaluate the rate of recurrence among patients with pheochromocytomas and sympathetic paragangliomas (PGLs; together PPGLs) and to identify predictors of recurrence (local recurrence and/or metastatic disease). Methods: This retrospective multicenter study included information of 303 patients with PPGLs in follow-up in 19 Spanish tertiary hospitals. Recurrent disease was defined by the development of local recurrence and/or metastatic disease after initial complete surgical resection. Results: A total of 303 patients with PPGLs that underwent 311 resections were included (288 pheochromocytomas and 15 sympathetic PGLs). After a median follow-up of 4.8 years (range 1-19), 24 patients (7.9%) had recurrent disease (3 local recurrence, 17 metastatic disease and 4 local recurrence followed by metastatic disease). The median time from the diagnosis of the PPGL to the recurrence was of 11.2 months (range 0.5-174) and recurrent disease cases distributed uniformly during the follow-up period. The presence of a pathogenic variant in SDHB gene (hazard ratio [HR] 13.3, 95% CI 4.20-41.92), higher urinary normetanephrine levels (HR 1.02 per each increase in standard deviation, 95% CI 1.01-1.03) and a larger tumor size (HR 1.01 per each increase in mm, 95% CI 1.00-1.02) were independently associated with disease recurrence. Conclusion: The recurrence of PPGLs occurred more frequently in patients with SDHB mutations, with larger tumors and with higher urinary normetanephrine levels. Since PPGL recurrence may occur at any time after the initial PPGL diagnosis is performed, we recommend performing a strict follow-up in all patients with PPGLs, especially in those patients with a higher risk of recurrent disease.

Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone.

OBJECTIVES: The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia. MATERIALS AND METHODS: Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network. RESULTS: The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established. DISCUSSION: The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.

OBJETIVOS: El objetivo principal de este estudio es discutir los procesos migratorios y la dinámica de poblamiento que moldearon la variabilidad genética de las poblaciones durante el poblamiento del Cono Sur, a través del análisis de mitogenomas completos de individuos del sur de Patagonia. MATERIALES Y MÉTODOS: Se obtuvieron mitogenomas completos mediante secuenciación masiva de dos individuos del Holoceno tardío (SAC 1-1-3 y SAC 1-1-4) enterrados en el mismo chenque en la Cuenca del Lago Salitroso (provincia de Santa Cruz, Argentina). Para evaluar las afinidades matrilineales con otros haplotipos, se realizaron reconstrucciones filogenéticas de máxima verosimilitud y bayesianas, así como una red mediana de haplotipos. RESULTADOS: Los mitogenomas fueron asignados a los haplogrupos B2 y B2b, exhibiendo una profundidad de secuenciación promedio de 54X y 89X (cobertura ≥1X de 98,6% y 100%), y un elevado número de diferencias nucleotídicas entre ellos. Los análisis filogenéticos mostraron una relación relativamente estrecha entre el haplotipo encontrado en el SAC 1-1-4 y los recuperados de un individuo del Holoceno Medio de Laguna Chica (provincia de Buenos Aires), y de un grupo de individuos de la costa peruana. Para el SAC 1-1-3, no se establecieron relaciones claras con ningún otro haplotipo. DISCUSIÓN: La gran divergencia entre los haplotipos presentados en este estudio sugiere gran variabilidad en el acervo genético fundador, o bien un enriquecimiento posterior por contacto biológico frecuente con otras poblaciones. Nuestros resultados destacan la persistencia de señales genéticas relacionadas con las primeras oleadas de poblamiento de Sudamérica, lo que sugiere que el poblamiento regional del extremo sur del continente ha sido mucho más complejo de lo que se pensaba inicialmente.

Arabidopsis subtilases promote defense-related pectin methylesterase activity and robust immune responses to botrytis infection.

Plants involve a fine modulation of pectin methylesterase (PME) activity against microbes. PME activity can promote the cell wall stiffening and the production of damage signals able to induce defense responses and plant resistance to pathogens. However, the molecular mechanisms underlying PME activation during disease remain largely unknown. In this study, we explored the role of subtilases (SBTs) as PME activators in Arabidopsis immunity. By using biochemical and reverse genetic approaches, we found that the expression of SBT3.3 and SBT3.5 influences the induction of defense-related PME activity and resistance to the fungus Botrytis cinerea. Arabidopsis sbt3.3 and sbt3.5 knockout mutants showed decreased induction of PME activity and increased susceptibility to the fungus. SBT3.3 expression was stimulated by oligogalacturonides. Overexpression of SBT3.3 overactivated PME activity during fungal infection and enhanced resistance to B. cinerea. A negative correlation was observed between SBT3.3 expression and cell wall methyl ester content in the genotypes analyzed after B. cinerea infection. Increased expression of defense-related genes, including PAD3, CYP81F2 and WAK2, was also revealed in SBT3.3 overexpressing lines. We also demonstrated that SBT3.3 and pro-PME17 are both secreted into the cell wall using distinct protein secretion pathways and different kinetics. Our results propose SBT3.3 and SBT3.5 as modulators of PME activity in Arabidopsis against Botrytis to promptly boost immunity limiting the growth-defense trade-off.

Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq) Technology.

Double digest restriction-site associated DNA sequencing (ddRADseq) technology combines genome reduced representation by digestion with two restriction enzymes and next generation sequencing (NGS) to obtain thousands of markers (SNP, SSR, and InDels) and genotype tens to hundreds of samples simultaneously. In this chapter, we describe a 96-plex derived ddRADseq protocol that can be set up to obtain different depth of coverage per locus and can be exploited to model and non-model plant species.

Genetic Study in Pheochromocytoma: Is It Possible to Stratify the Risk of Hereditary Pheochromocytoma?

INTRODUCTION: It is estimated that 30-40% of patients with apparently sporadic pheochromocytomas (PHEOs) have an inherited predisposition syndrome. The aim of our study was to develop a predictive model of hereditary PHEO based on the clinical, hormonal, and radiological features present at the diagnosis of patients with PHEOs. METHODS: A retrospective multicenter cohort study of patients with PHEOs with available genetic study from 18 tertiary hospitals. Clinical, biochemical, and radiological features were used to build a multivariate logistic regression model. The estimation of all possible equations was used to select the model with the best diagnostic accuracy (lower Akaike index). RESULTS: A total of 245 patients were included: 169 (69.0%) patients with sporadic PHEOs and 76 (31%) with hereditary PHEOs. The parsimonious predictive model with the highest diagnostic accuracy for the prediction of hereditary PHEO combined the variables age, non-cardiovascular disease, urinary norepinephrine levels, and tumor size. The area under the ROC curve of this model was 0.800 (0.705-0.887). Based on the predictive model, the probability of hereditary PHEO in patients older than 60 years with cardiovascular disease, high levels of urinary norepinephrine and unilateral PHEOs >60 mm was <2%. And if the age was above 80 years, lower than 1%. The probability of sporadic PHEO linearly increased with age (MH Test for linear Trend: χ2 (1) = 30.05; p < 0.001). CONCLUSION: In certain populations such as old patients with cardiovascular disease, with high levels of urinary norepinephrine and large tumors in which the probability of hereditary PHEO is very low, genetic testing could be avoided in the absence of specific suspicion.

Assessing the hidden diversity underlying consensus sequences of SARS-CoV-2 using VICOS, a novel bioinformatic pipeline for identification of mixed viral populations.

INTRODUCTION: Coinfection with two SARS-CoV-2 viruses is still a very understudied phenomenon. Although next generation sequencing methods are very sensitive to detect heterogeneous viral populations in a sample, there is no standardized method for their characterization, so their clinical and epidemiological importance is unknown. MATERIAL AND METHODS: We developed VICOS (Viral COinfection Surveillance), a new bioinformatic algorithm for variant calling, filtering and statistical analysis to identify samples suspected of being mixed SARS-CoV-2 populations from a large dataset in the framework of a community genomic surveillance. VICOS was used to detect SARS-CoV-2 coinfections in a dataset of 1,097 complete genomes collected between March 2020 and August 2021 in Argentina. RESULTS: We detected 23 cases (2%) of SARS-CoV-2 coinfections. Detailed study of VICOS's results together with additional phylogenetic analysis revealed 3 cases of coinfections by two viruses of the same lineage, 2 cases by viruses of different genetic lineages, 13 were compatible with both coinfection and intra-host evolution, and 5 cases were likely a product of laboratory contamination. DISCUSSION: Intra-sample viral diversity provides important information to understand the transmission dynamics of SARS-CoV-2. Advanced bioinformatics tools, such as VICOS, are a necessary resource to help unveil the hidden diversity of SARS-CoV-2.

ddRADseq-mediated detection of genetic variants in sugarcane.

KEY MESSAGE: The article presents an optimization of the key parameters for the identification of SNPs in sugarcane using a GBS protocol based on two Illumina NextSeq and NovaSeq platforms. Sugarcane (Saccharum sp.), a world-wide known feedstock for sugar production, bioethanol, and energy, has an extremely complex genome, being highly polyploid and aneuploid. A double-digestion restriction site-associated DNA sequencing protocol (ddRADseq) was tested in four commercial sugarcane hybrids and one high-fibre biotype for the detection of single nucleotide polymorphisms (SNPs). In this work we tested two Illumina sequencing platforms, read size (70 vs. 150 bp), different sequencing coverage per individual (medium and high coverage), and single-reads versus paired-end reads. We also explored different variant calling strategies (with and without reference genome) and filtering schemes [combining two minor allele frequencies (MAFs) with three depth of coverage thresholds]. For the discovery of a large number of novel SNPs in sugarcane, we recommend longer size and paired-end reads, medium sequencing coverage per individual and Illumina platform NovaSeq6000 for a cost-effective approach, and filter parameters of lower MAF and higher depth coverages thresholds. Although the de novo analysis retrieved more SNPs, the reference-based method allows downstream characterization of variants. For the two best performing matrices, the number of SNPs per chromosome correlated positively with chromosome length, demonstrating the presence of variants throughout the genome. Multivariate comparisons, with both matrices, showed closer relationships among commercial hybrids than with the high-fibre biotype. Functional analysis of the SNPs demonstrated that more than half of them landed within regulatory regions, whereas the other half affected coding, intergenic and intronic regions. Allelic distances values were lower than 0.07 when analysing two replicated genotypes, confirming the protocol robustness.

Phenotypic and genetic characterization of Africanized Apis mellifera colonies with natural tolerance to Varroa destructor and contrasting defensive behavior.

Africanized Apis mellifera colonies with promising characteristics for beekeeping have been detected in northern Argentina (subtropical climate) and are considered of interest for breeding programs. Integral evaluation of this feral material revealed high colony strength and resistance/tolerance to brood diseases. However, these Africanized honeybees (AHB) also showed variable negative behavioral traits for beekeeping, such as defensiveness, tendency to swarm and avoidance behavior. We developed a protocol for the selection of AHB stocks based on defensive behavior and characterized contrasting colonies for this trait using NGS technologies. For this purpose, population and behavioral parameters were surveyed throughout a beekeeping season in nine daughter colonies obtained from a mother colony (A1 mitochondrial haplotype) with valuable characteristics (tolerance to the mite Varroa destructor, high colony strength and low defensiveness). A Defensive Behavior Index was developed and tested in the colonies under study. Mother and two daughter colonies displaying contrasting defensive behavior were analyzed by ddRADseq. High-quality DNA samples were obtained from 16 workers of each colony. Six pooled samples, including two replicates of each of the three colonies, were processed. A total of 12,971 SNPs were detected against the reference genome of A. mellifera, 142 of which showed significant differences between colonies. We detected SNPs in coding regions, lncRNA, miRNA, rRNA, tRNA, among others. From the original data set, we also identified 647 SNPs located in protein-coding regions, 128 of which are related to 21 genes previously associated with defensive behavior, such as dop3 and dopR2, CaMKII and ADAR, obp9 and obp10, and members of the 5-HT family. We discuss the obtained results by considering the influence of polyandry and paternal lineages on the defensive behavior in AHB and provide baseline information to use this innovative molecular approach, ddRADseq, to assist in the selection and evaluation of honey bee stocks showing low defensive behavior for commercial uses.

An Analysis of Noise in Multi-Bit ΣΔ Modulators with Low-Frequency Input Signals.

Digital and smart sensors are commonly implemented using multi-bit ΣΔ Modulators. Undesired signals can be present at the ADC input, such as low-frequency signals with medium or high amplitude, as a consequence of mechanical artifacts in the MEMS and/or temporary signal overload. Simulations and measurements of those sensors with such signals show temporary increments of in-band noise power. This paper investigates the factors that produce this transient performance loss. Interestingly, noise increments happen when the modulator is forced to toggle between three adjacent levels and is not correlated with the typical tonal behavior of ΣΔ Modulators. Hence, the sensor performance is sensitive to some specific input patterns even if tonal behavior is decreased by dithering the input of the ADC. Different error sources, such as the mismatch between DAC cells, loop filter linearity error, and quantization error, contribute to the observed noise increments. Our aim is to analyze each of these error sources to understand and quantify in-band noise power increments, and to desensitize the ADC from the undesired input patterns. Some estimation equations are proposed and verified through extensive simulations, by means of deterministic and stochastic methods. These equations are influenced by some modulator parameters and can be used to optimize them in order to reduce such in-band noise power increments.

Energy Deposition around Swift Carbon-Ion Tracks in Liquid Water.

Energetic carbon ions are promising projectiles used for cancer radiotherapy. A thorough knowledge of how the energy of these ions is deposited in biological media (mainly composed of liquid water) is required. This can be attained by means of detailed computer simulations, both macroscopically (relevant for appropriately delivering the dose) and at the nanoscale (important for determining the inflicted radiobiological damage). The energy lost per unit path length (i.e., the so-called stopping power) of carbon ions is here theoretically calculated within the dielectric formalism from the excitation spectrum of liquid water obtained from two complementary approaches (one relying on an optical-data model and the other exclusively on ab initio calculations). In addition, the energy carried at the nanometre scale by the generated secondary electrons around the ion's path is simulated by means of a detailed Monte Carlo code. For this purpose, we use the ion and electron cross sections calculated by means of state-of-the art approaches suited to take into account the condensed-phase nature of the liquid water target. As a result of these simulations, the radial dose around the ion's path is obtained, as well as the distributions of clustered events in nanometric volumes similar to the dimensions of DNA convolutions, contributing to the biological damage for carbon ions in a wide energy range, covering from the plateau to the maximum of the Bragg peak.

Cardiorespiratory function of patients undergoing surgical correction of Scheuermann's hyperkyphosis.

The aim of this study was to analyze the impact of surgical correction of the thoracic deformity on the cardiorespiratory function of patients with moderate-severe Scheuermann's hyperkyphosis (SK). A series of 23 adolescents with SK who underwent surgery through an only posterior approach using all pedicle screw constructs were included in the study. Cardiorespiratory parameters were measured during a maximal exercise tolerance test before and 2 years after surgery. Heart rate, oxygen saturation (SatO2), maximum oxygen uptake (VO2 max), ventilatory capacity at maximal exercise (VEmax), and energy costs were recorded. There were statistically significant differences in the forced vital capacity (FVC) (P < 0.05), total VO2max (ml/min) (P < 0.01), maximum expired volume (VEmax) per minute (P < 0.01) and cardiovascular efficiency (HR/VO2 ratio) (P < 0.05). None of these changes were clinically relevant. There were no changes in the VO2max per kg of body mass. The magnitude of the kyphosis correction did not correlate with the change in normalized VO2max or VEmax. In conclusion, patients with moderate-severe SK improve their baseline respiratory limitations and the tolerance to maximum exercise 2 years after surgery. However, the slight cardiorespiratory functional improvements should not necessarily be attributed to the surgery, and could also be caused solely by the residual growth of the lungs and thorax. Furthermore, respiratory functional changes are under thresholds considered as clinically relevant.

Electronic excitation spectra of cerium oxides: from ab initio dielectric response functions to Monte Carlo electron transport simulations.

Nanomaterials made of cerium oxides CeO2 and Ce2O3 have a broad range of applications, from catalysts in automotive, industrial or energy operations to promising materials to enhance hadrontherapy effectiveness in oncological treatments. To elucidate the physico-chemical mechanisms involved in these processes, it is of paramount importance to know the electronic excitation spectra of these oxides, which are obtained here through high-accuracy linear-response time-dependent density functional theory calculations. In particular, the macroscopic dielectric response functions  of both bulk CeO2 and Ce2O3 are derived, which compare remarkably well with the available experimental data. These results stress the importance of appropriately accounting for local field effects to model the dielectric function of metal oxides. Furthermore, we reckon the energy loss functions Im(-1/) of the materials, including the accurate evaluation of the momentum transfer dispersion from first-principles calculations. In this respect, by using Mermin-type parametrization we are able to model the contribution of different electronic excitations to the dielectric loss function. Finally, from the knowledge of the electron inelastic mean free path, together with the elastic mean free path provided by the relativistic Mott theory, we carry out statistical Monte Carlo (MC) electron transport simulations to reproduce the major features of the reported experimental reflection electron energy loss (REEL) spectra of cerium oxides. The good agreement with REEL experimental data strongly supports our approach based on MC modelling, whose main inputs were obtained using ab initio calculated electronic excitation spectra in a broad range of momentum and energy transfers.

Opposing roles of plant laticifer cells in the resistance to insect herbivores and fungal pathogens.

More than 12,000 plant species (ca. 10% of flowering plants) exude latex when their tissues are injured. Latex is produced and stored in specialized cells named "laticifers". Laticifers form a tubing system composed of rows of elongated cells that branch and create an internal network encompassing the entire plant. Laticifers constitute a recent evolutionary achievement in ecophysiological adaptation to specific natural environments; however, their fitness benefit to the plant still remains to be proven. The identification of Euphorbia lathyris mutants (pil mutants) deficient in laticifer cells or latex metabolism, and therefore compromised in latex production, allowed us to test the importance of laticifers in pest resistance. We provided genetic evidence indicating that laticifers represent a cellular adaptation for an essential defense strategy to fend off arthropod herbivores with different feeding habits, such as Spodoptera exigua and Tetranychus urticae. In marked contrast, we also discovered that a lack of laticifer cells causes complete resistance to the fungal pathogen Botrytis cinerea. Thereafter, a latex-derived factor required for conidia germination on the leaf surface was identified. This factor promoted disease susceptibility enhancement even in the non-latex-bearing plant Arabidopsis. We speculate on the role of laticifers in the co-evolutionary arms race between plants and their enemies.

Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographical structuring of nuclear gene pools.

BACKGROUND AND AIMS: The number of plastome sequences has increased exponentially during the last decade. However, there is still little knowledge of the levels and distribution of intraspecific variation. The aims of this study were to estimate plastome diversity within Zea mays and analyse the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers. METHODS: We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of next-generation sequencing (NGS) and used them in combination with data from public repositories. After quality filtering, the curated data were employed to search for single-nucleotide polymorphisms, indels and chloroplast simple sequence repeats. Exact permutational contingency tests were performed to assess associations between plastome and nuclear variation. Network and Bayesian phylogenetic analyses were used to infer evolutionary relationships among haplotypes. KEY RESULTS: Our analyses identified a total of 124 polymorphic plastome loci, with the intergenic regions psbE-rps18, petN-rpoB, trnL_UAG-ndhF and rpoC2-atpI exhibiting the highest marker densities. Although restricted in number, these markers allowed the discrimination of 27 haplotypes in a total of 51 Zea mays individuals. Andean and lowland South American landraces differed significantly in haplotype distribution. However, overall differentiation patterns were not informative with respect to subspecies diversification, as evidenced by the scattered distribution of maize and teosinte plastomes in both the network and Bayesian phylogenetic reconstructions. CONCLUSIONS: Knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers.

Excitation and ionisation cross-sections in condensed-phase biomaterials by electrons down to very low energy: application to liquid water and genetic building blocks.

Electronic excitations and ionisations produced by electron impact are key processes in the radiation-induced damage mechanisms in materials of biological relevance, underlying important medical and technological applications, including radiotherapy, radiation protection in manned space missions and nanodevice fabrication techniques. However, experimentally measuring all the necessary electronic interaction cross-sections for every relevant material is an arduous task, so it is necessary having predictive models, sufficiently accurate yet easily implementable. In this work we present a model, based on the dielectric formalism, to provide reliable ionisation and excitation cross-sections for electron-impact on complex biomolecular media, considering their condensed-phase nature. We account for the indistinguishability and exchange between the primary beam and excited electrons, for the molecular electronic structure effects in the electron binding, as well as for low-energy corrections to the first Born approximation. The resulting approach yields total ionisation cross-sections, energy distributions of secondary electrons, and total electronic excitation cross-sections for condensed-phase biomaterials, once the electronic excitation spectrum is known, either from experiments or from a predictive model. The results of this methodology are compared with the available experimental data in water and DNA/RNA molecular building blocks, showing a very good agreement and a great predictive power in a wide range of electron incident energies, from the large values characteristic of electron beams down to excitation threshold. The proposed model constitutes a very useful procedure for computing the electronic interaction cross-sections for arbitrary biological materials in a wide range of electron incident energies.

Relative Role of Physical Mechanisms on Complex Biodamage Induced by Carbon Irradiation.

The effective use of swift ion beams in cancer treatment (known as hadrontherapy) as well as appropriate protection in manned space missions rely on the accurate understanding of the energy delivery to cells that damages their genetic information. The key ingredient characterizing the response of a medium to the perturbation induced by charged particles is its electronic excitation spectrum. By using linear-response time-dependent density functional theory, we obtained the energy and momentum transfer excitation spectrum (the energy-loss function, ELF) of liquid water (the main constituent of biological tissues), which was in excellent agreement with experimental data. The inelastic scattering cross sections obtained from this ELF, together with the elastic scattering cross sections derived by considering the condensed phase nature of the medium, were used to perform accurate Monte Carlo simulations of the energy deposited by swift carbon ions in liquid water and carried away by the generated secondary electrons, producing inelastic events such as ionization, excitation, and dissociative electron attachment (DEA). The latter are strongly correlated with cellular death, which is scored in sensitive volumes with the size of two DNA convolutions. The sizes of the clusters of damaging events for a wide range of carbon-ion energies, from those relevant to hadrontherapy up to those for cosmic radiation, predict with unprecedented statistical accuracy the nature and relative magnitude of the main inelastic processes contributing to radiation biodamage, confirming that ionization accounts for the vast majority of complex damage. DEA, typically regarded as a very relevant biodamage mechanism, surprisingly plays a minor role in carbon-ion induced clusters of harmful events.