Dislocation-induced thermal transport anisotropy in single-crystal group-III nitride films.

Dislocations, one-dimensional lattice imperfections, are common to technologically important materials such as III-V semiconductors, and adversely affect heat dissipation in, for example, nitride-based high-power electronic devices. For decades, conventional nonlinear elasticity models have predicted that this thermal resistance is only appreciable when the heat flux is perpendicular to the dislocations. However, this dislocation-induced anisotropic thermal transport has yet to be seen experimentally. Using time-domain thermoreflectance, we measure strong thermal transport anisotropy governed by highly oriented threading dislocation arrays throughout micrometre-thick, single-crystal indium nitride films. We find that the cross-plane thermal conductivity is almost tenfold higher than the in-plane thermal conductivity at 80 K when the dislocation density is ~3 × 1010 cm-2. This large anisotropy is not predicted by conventional models. With enhanced understanding of dislocation-phonon interactions, our results may allow the tailoring of anisotropic thermal transport with line defects, and could facilitate methods for directed heat dissipation in the thermal management of diverse device applications.

Non-stochastic behavior in sodium chlorate crystallization.

NaClO3 is achiral in solution. If crystallization is performed under a static set-up, it is recognized that the stochastic nucleation probability results in a racemic mixture of the conglomerate. In this paper, we report a reexamination of the crystallization of NaClO3 from static solution in petri dishes that was conducted over a number of years and is based on the count and analysis of several thousand d- vs. l-NaClO3 crystals. Remarkably, instead of an expected nearly 50/50 coin-tossing situation for the d/l crystal frequency, in most of our experiments a statistically significant bias in favor of d- over l-NaClO3 crystals was found. The experiments also showed that the NaClO3 system was relatively insensitive regarding the intentional addition of a variety of optically active agents. Only in some cases, the persisting d-bias observed in the unseeded experiments slightly increased upon the presence of such additives. Nevertheless, experiments in plastic petri dishes or in presence of fungal spores were able to reverse this bias. A literature survey shows that mainly d-directed non-stochastic behavior in the NaClO3 system has been previously observed in other laboratory settings and by the application of different crystallization techniques. So far, the kind of chiral influence that could be at the origin of the observed bias remains unknown. After the examination of several possible chiral influences of physical, chemical and biological origin, we carefully consider the presence of bio-contaminants as most likely for the cause of this effect.

Antisite Pairs Suppress the Thermal Conductivity of BAs.

BAs was predicted to have an unusually high thermal conductivity with a room temperature value of 2000 W m^{-1} K^{-1}, comparable to that of diamond. However, the experimentally measured thermal conductivity of BAs single crystals is still lower than this value. To identify the origin of this large inconsistency, we investigate the lattice structure and potential defects in BAs single crystals at the atomic scale using aberration-corrected scanning transmission electron microscopy (STEM). Rather than finding a large concentration of As vacancies (V_{As}), as widely thought to dominate the thermal resistance in BAs, our STEM results show an enhanced intensity of some B columns and a reduced intensity of some As columns, suggesting the presence of antisite defects with As_{B} (As atom on a B site) and B_{As} (B atom on an As site). Additional calculations show that the antisite pair with As_{B} next to B_{As} is preferred energetically among the different types of point defects investigated and confirm that such defects lower the thermal conductivity for BAs. Using a concentration of 1.8(8)% (6.6±3.0×10^{20} cm^{-3} in density) for the antisite pairs estimated from STEM images, the thermal conductivity is estimated to be 65-100 W m^{-1} K^{-1}, in reasonable agreement with our measured value. Our study suggests that As_{B}-B_{As} antisite pairs are the primary lattice defects suppressing thermal conductivity of BAs. Possible approaches are proposed for the growth of high-quality crystals or films with high thermal conductivity. Employing a combination of state-of-the-art synthesis, STEM characterization, theory, and physical insight, this work models a path toward identifying and understanding defect-limited material functionality.

Analysis of somaclonal variation in transgenic and regenerated plants of Arabidopsis thaliana using methylation related metAFLP and TMD markers.

KEY MESSAGE: We provide evidence that nucleotide sequence and methylation status changes occur in the Arabidopsis genome during in vitro tissue culture at a frequency high enough to represent an important source of variation. Somaclonal variation is a general consequence of the tissue culture process that has to be analyzed specifically when regenerated plants are obtained in any plant species. Currently, there are few studies about the variability comprising sequence changes and methylation status at the DNA level, generated by the culture of A. thaliana cells and tissues. In this work, two types of highly reproducible molecular markers, modified methylation sensitive AFLP (metAFLP) and transposon methylation display (TMD) have been used for the first time in this species to analyze the nucleotide and cytosine methylation changes induced by transformation and tissue culture protocols. We found significantly higher average methylation values (7.5%) in regenerated and transgenic plants when compared to values obtained from seed derived plants (3.2%) and that the main component of the somaclonal variation present in Arabidopsis clonal plants is genetic rather than epigenetic. However, we have found that the Arabidopsis regenerated and transgenic plants had a higher number of non-fully methylated sites flanking transposable elements than the control plants, and therefore, their mobilization can be facilitated. These data provide further evidence that changes in nucleotide sequence and methylation status occur in the Arabidopsis genome during in vitro tissue culture frequently enough to be an important source of variation in this species.

Genetic variation of the endangered Gentiana lutea L. var. aurantiaca (Gentianaceae) in populations from the Northwest Iberian Peninsula.

Gentiana lutea L. (G. lutea L.) is an endangered plant, patchily distributed along the mountains of Central and Southern Europe. In this study, inter-simple sequence repeat (ISSR) markers were used to investigate the genetic variation in this species within and among populations of G. lutea L. var. aurantiaca of the Cantabrian Mountains (Northwest Iberian Peninsula). Samples of G. lutea L. collected at different locations of the Pyrenees and samples of G. lutea L. subsp. vardjanii of the Dolomites Alps were also analyzed for comparison. Using nine ISSR primers, 106 bands were generated, and 89.6% of those were polymorphic. The populations from the Northwest Iberian Peninsula were clustered in three different groups, with a significant correlation between genetic and geographic distances. Gentiana lutea L. var. aurantiaca showed 19.8% private loci and demonstrated a remarkable level of genetic variation, both among populations and within populations; those populations with the highest level of isolation show the lowest genetic variation within populations. The low number of individuals, as well as the observed genetic structure of the analyzed populations makes it necessary to protect them to ensure their survival before they are too small to persist naturally.

Differential rRNA genes expression in bread wheat and its inheritance.

The expression of the ribosomal RNA (rRNA) genes from rye, located within the nucleolus organizer regions (NORs), is repressed by cytosine methylation in wheat x rye hybrids and in triticale, as consequence of nucleolar dominance. Our previous study revealed that bread wheat cultivars with a maximum number of four Ag-NORs presented high level of rDNA cytosine methylation when compared to others with a maximum of six Ag-NORs. In order to evaluate the inheritance of the Ag-NORs number and NOR methylation patterns, we produced F1 hybrids between bread wheat cultivars with four Ag-NORs and bread wheat cultivars with six Ag-NORs (in the direct and reciprocal senses). The F2 progenies of these F1 hybrids were also evaluated for the NOR number and methylation patterns. Parent bread wheat cultivars with a maximum of four Ag-NORs after treated with 5-azacytidine evidenced a maximum of six Ag-NORs per metaphase cell and a maximum of six nucleoli per interphase nucleus, confirming that the expression of the rRNA genes in bread wheat is related to cytosine methylation. Most of the F1 hybrids showed a maximum number of four or six Ag-NORs, similarly to that of the female parent suggesting a non-mendelian inheritance, while other hybrids presented four or six Ag-NORs in both senses of the cross. The F1 NOR methylation patterns showed some fragments common to their parents but also novel fragments suggesting genomic and/or chromosome rearrangements after hybridization. Despite the different NOR patterns among the parents, an invariable NOR pattern was found among the F1 plants suggesting a tendency to stability, which was also transmitted to the F2. The F2 progenies showed plants with a maximum of four, five and/or six Ag-NORs. The ratio of plants with four, five and/or six Ag-NORs per F2 progeny was variable and did not follow any specific mendelian proportion. These results allowed us to suggest that the inheritance of the number of Ag-NORs by the F1 and F2 plants did not follow any mendelian inheritance and were not correlated to NOR methylation patterns in contrast to what was verified for their parents.

The phonon quantum of thermal conductance: Are simulations and measurements estimating the same quantity?

The thermal conductance quantum is a fundamental quantity in quantum transport theory. However, two decades after its first reported measurements and calculations for phonons in suspended nanostructures, reconciling experiments and theory remains elusive. Our massively parallel calculations of phonon transport in micrometer-sized three-dimensional structures suggest that part of the disagreement between theory and experiment stems from the inadequacy of macroscopic concepts to analyze the data. The computed local temperature distribution in the wave ballistic nonequilibrium regime shows that the spatial placement and dimensions of thermometers, heaters, and supporting microbeams in the suspended structures can noticeably affect the thermal conductance's measured values. In addition, diffusive transport assumptions made in the data analysis may result in measured values that considerably differ from the actual thermal conductance of the structure. These results urge for experimental validation of the suitability of diffusive transport assumptions in measuring devices operating at sub-kelvin temperatures.

Bioinformatics Insights on the Physicochemical Properties of SCN5A Mutant Proteins Associated with the Brugada Syndrome.

BACKGROUND: The Brugada syndrome (BrS) is a heart rhythm condition that is commonly associated with a strong predisposition for sudden cardiac death. Malignant ventricular arrhythmias could occur secondary to the dysfunction of the cardiac sodium voltage-gated Na(v)1.5 channel (SCN5A). OBJECTIVE: This study aimed to perform a multiparametric computational analysis of the physicochemical properties of SCN5A mutants associated with BrS using a set of bioinformatics tools. METHODS: In-house algorithms were calibrated to calculate, in a double-blind test, the Polarity Index Method (PIM) profile and protein intrinsic disorder predisposition (PIDP) profile of each sequence, and computer programs specialized in the genomic analysis were used. RESULTS: Specific regularities in the charge/polarity and PIDP profile of the SCN5A mutant proteins enabled the re-creation of the taxonomy, allowing us to propose a bioinformatics method that takes advantage of the PIM profile to identify this group of proteins from their sequence. CONCLUSION: Bioinformatics programs could reproduce characteristic PIM and PIDP profiles of the BrS-related SCN5A mutant proteins. This information can contribute to a better understanding of these altered proteins.

Bioinformatics-based Characterization of the Sequence Variability of Zika Virus Polyprotein and Envelope Protein (E).

Background: Zika virus, which is widely spread and infects humans through the bites of Aedes albopictus and Aedes aegypti female mosquitoes, represents a serious global health issue. Objective: The objective of the present study is to computationally characterize Zika virus polyproteins (UniProt Name: PRO_0000443018 [residues 1-3423], PRO_0000445659 [residues 1-3423] and PRO_0000435828 [residues 1-3419]) and their envelope proteins using their physico-chemical properties. Methods: To achieve this, the Polarity Index Method (PIM) profile and the Protein Intrinsic Disorder Predisposition (PIDP) profile of 3 main groups of proteins were evaluated: structural proteins extracted from specific Databases, Zika virus polyproteins, and their envelope proteins (E) extracted from UniProt Database. Once the PIM profile of the Zika virus envelope proteins (E) was obtained and since the Zika virus polyproteins were also identified with this profile, the proteins defined as "reviewed proteins" extracted from the UniProt Database were searched for the similar PIM profile. Finally, the difference between the PIM profiles of the Zika virus polyproteins and their envelope proteins (E) was tested using 2 non-parametric statistical tests. Results: It was found and tested that the PIM profile is an efficient discriminant that allows obtaining a "computational fingerprint" of each Zika virus polyprotein from its envelope protein (E). Conclusion: PIM profile represents a computational tool, which can be used to effectively discover Zika virus polyproteins from Databases, from their envelope proteins (E) sequences.

The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high-density linkage maps in comparative mapping and synteny analysis.

Powdery mildews are major diseases for a range of crops. The loss of function of specific Mildew Locus O (MLO) genes has long been associated with pre-haustorial plant resistance to powdery mildew and has proven to be durable in several species. Erysiphe pisi is the major causal agent of powdery mildew in pea (Pisum sativum L.) and in the closely related Lathyrus sativus L. and Lathyrus cicera L. PsMLO1 has been extensively studied in pea. However, no MLO gene family members have been isolated and characterized in Lathyrus species so far. In this study, MLO1 genes were isolated and characterized in L. sativus and L. cicera genotypes with varied levels of partial resistance against powdery mildew. Phylogenetic analyses confirmed that Lathyrus MLO1 belongs to Clade V, like all dicot MLO proteins associated with powdery mildew susceptibility. A L. sativus recombinant inbred line population (RIL) was genotyped by sequencing to develop a high-density L. sativus genetic linkage map. DNA sequence polymorphisms between the analyzed genotypes allowed the location of MLO1 in the newly developed L. sativus RIL genetic linkage map. Subsequent comparative mapping between L. sativus and L. cicera genetic maps and P. sativum, Lens culinaris Medik., and Medicago truncatula Gaertn. reference genomes revealed important aspects of the conservation of the MLO1 locus position and of the overall chromosomal rearrangements occurring during legume evolution, with relevance to legume disease resistance breeding programs.

Cost-effectiveness analysis of apixaban versus vitamin K antagonists for antithrombotic therapy in patients with atrial fibrillation after acute coronary syndrome or percutaneous coronary intervention in Spain.

BACKGROUND/OBJECTIVE: AUGUSTUS trial demonstrated that, for patients with atrial fibrillation (AF) having acute coronary syndrome (ACS) or undergoing percutaneous coronary intervention (PCI), an antithrombotic regimen with apixaban and P2Y12 resulted in less bleeding, fewer hospitalizations, and similar ischemic events than regimens including a vitamin K antagonist (VKA), aspirin, or both. This study objective was to evaluate long-term health and economic outcomes and the cost-effectiveness of apixaban over VKA, as a treatment option for patients with AF having ACS/PCI. METHODS: A lifetime Markov cohort model was developed comparing apixaban versus VKA across multiple treatment strategies (triple [with P2Y12 + aspirin] or dual [with P2Y12] therapy followed by monotherapy [apixaban or VKA]; triple followed by dual and then monotherapy; dual followed by monotherapy). The model adopted the Spanish healthcare perspective, with a 3-month cycle length and costs and health outcomes discounted at 3%. RESULTS: Treatment with apixaban resulted in total cost savings of €883 and higher life years (LYs) and quality-adjusted LYs (QALYs) per patient than VKA (net difference, LYs: 0.13; QALYs: 0.11). Bleeding and ischemic events (per 100 patients) were lower with apixaban than VKA (net difference, -13.9 and -1.8, respectively). Incremental net monetary benefit for apixaban was €3,041, using a willingness-to-pay threshold of €20,000 per QALY. In probabilistic sensitivity analysis, apixaban was dominant in the majority of simulations (92.6%), providing additional QALYs at lower costs than VKA. CONCLUSIONS: Apixaban was a dominant treatment strategy than VKA from both the Spanish payer's and societal perspectives, regardless of treatment strategy considered.

Cost and burden of poor anticoagulation control with vitamin K antagonists in patients with nonvalvular atrial fibrillation in Spain.

INTRODUCTION AND OBJECTIVES: The aim of this analysis was to evaluate the burden and cost of complications due to poor anticoagulation control in patients with nonvalvular atrial fibrillation (NVAF) treated with vitamin K antagonists (VKA) in Spain. METHODS: An analytical model was used to estimate annual differences in ischemic stroke, major bleeding, deaths, costs, and potential years of life lost between patients with poor anticoagulation control (time in therapeutic range <65%) and adequate control (time in therapeutic range ≥ 65%) with a 1-year time horizon. Information on the target population (patients ≥ 65 years), event rates, and costs were obtained from national sources. Direct costs in euros (2018) were included from the perspective of the national health system (NHS) and direct and indirect costs from the societal perspective. A sensitivity analysis was performed with post-hoc data from the SPORTIF III/V trials. RESULTS: We analyzed a hypothetical cohort of 594 855 patients, 48.3% with poor anticoagulation control, with an increase of 2321 ischemic strokes, 2236 major bleeding events and 14 463 deaths, and an annual incremental cost between €29 578 306 from the NHS perspective and €75 737 451 from the societal perspective. The annual impact of mortality was 170 502 potential years of life lost. The results of the sensitivity analysis showed that the annual cost would reach €97 787 873 from the societal perspective. CONCLUSIONS: Poor anticoagulation control with AVK has a strong impact on loss of health and on increased spending for the NHS.

Interplay of electrical forces for alignment of sub-100 nm electrospun nanofibers on insulator gap collectors.

We present a quantitative design methodology for optimizing insulator gap width, gap resistivity, and collector to needle height for the alignment of sub-100 nm electrospun nanofibers at insulator gaps of metal collectors. Enhancement of the spatial extent of alignment forces at insulator gaps, due to the concerted action of attractive stretching forces from the modified electric fields and repulsive forces from residual charges on undischarged fibers in the gap, is studied. At gap widths considerably smaller than the collector to needle height (<2%), the spatial extent of stretching forces is large as evidenced by successive reduction in nanofiber size with gap width; however, the low magnitude of repulsive forces limits the degree of nanofiber alignment. At successively larger gap widths less than the needle height, the spatial extent of the stretching forces is gradually restricted toward the metal-insulator edges, while the influence of repulsive forces is gradually extended across the rest of the spatial extent of the gap, to cause enhanced nanofiber alignment through the concerted action of these forces. At gap widths greater than the needle height, the limited spatial extent and lowered maximum value of the stretching forces at the metal-insulator edge reduces their influence on fiber stretching and alignment. The collection of sub-100 nm electrospun poly(lactic acid-co-glycolic acid) nanofibers with a good degree of alignment (≤10° deviation) is found to require intermediate size gaps (∼2% of needle height) of high resistivity (≥10(12) ohm-cm), to enhance the spatial extent of stretching forces while maintaining the dominance of repulsive forces due to residual charge across a majority of the spatial extent of the gap.

Cost-Effectiveness Analysis of Apixaban Versus Edoxaban in Patients with Atrial Fibrillation for Stroke Prevention.

OBJECTIVE: Our objective was to assess the cost effectiveness of apixaban versus edoxaban in the prevention of stroke and systemic embolism (SE) in patients with atrial fibrillation (AF) in Spain. METHODS: We customized a Markov model with ten health states to estimate the lifetime economic and clinical outcomes in 6-week cycles. The efficacy (clinical event rates per 100 patient-years) and safety data were derived from a pairwise indirect treatment comparison. The analysis was conducted from both the national health service (NHS) and societal perspectives, and included pharmaceutical costs (retail price plus value-added tax (VAT) and applicable national deductions) according to daily dosages (apixaban 10 mg (5 mg twice daily (bid)) and edoxaban 60 or 30 mg) and complications and disease-management costs, obtained from national databases. Utilities for quality-adjusted life-year (QALY) calculations reflected EuroQoL 5-Dimension scores in patients with AF. An annual discount rate of 3% was applied for costs (€, year 2019 values) and outcomes. RESULTS: In a 1000-patient cohort, apixaban 5 mg bid versus edoxaban 60 mg could avoid five strokes, six major bleedings and 29 clinically relevant non-major bleedings (CRNMBs). Compared with edoxaban 30 mg, apixaban could avoid 21 strokes and two SEs. An increase in bleedings was observed with apixaban (seven haemorrhagic strokes, 48 major bleedings and 17 CRNMBs). Apixaban yielded 0.04 additional QALYs compared with edoxaban 60 mg or 30 mg. Incremental costs/QALY were €9639.33 and €354.22 for apixaban versus edoxaban 60 mg and edoxaban 30 mg, respectively, from the NHS perspective and €7756.62 for apixaban versus edoxaban 60 mg from the societal perspective. Apixaban was dominant versus edoxaban 30 mg from the societal perspective. Sensitivity analyses confirmed the robustness of the model. CONCLUSIONS: This study suggests that apixaban 5 mg bid is a cost-effective alternative to edoxaban for stroke prevention in the AF population in Spain.

Standardizing Health Outcomes for Lung Cancer. Adaptation of the International Consortium for Health Outcomes Measurement Set to the Spanish Setting.

Purpose: Lung cancer (LC) and its treatment impose a significant burden on patients' life. However, patient-centered outcomes are rarely collected during patient follow-up. Filling this gap, the International Consortium for Health Outcomes Measurement (ICHOM) developed a standard set of variables for newly diagnosed LC patients. In order to facilitate the use of this standard set, the project aims to adapt it to the Spanish setting. Methods: The variables (instrument and periodicity) to be included in Spanish standard set were selected through consensus during 4 nominal groups (13 oncologists, 14 hospital pharmacists, 4 hospital managers and 3 LC patients), under the supervision of a Scientific Committee (1 oncologist, 3 hospital pharmacists, 2 LC patients advocates). Results: The variables agreed upon included: (1) case-mix: demographic [age, sex, education and social-family support], clinical [weight loss, smoking status, comorbidities (Charlson index), pulmonary function (FEV-1)], tumor [histology, clinical, and pathological stage (TNM), EGFR, ALK, ROS-1, PD-L1] and treatment factors [intent and completion] and (2) outcomes: degree of health [performance status (ECOG) and quality-of-life (EQ-5D, LCSS)], survival [overall survival and cause of death], quality of death [place of death, end-of-life care and palliative care, death aligned with living will], treatment complications, and others [date of diagnosis and treatment initiation, productivity loss (sick leave)]. Conclusion: The adaptation of ICHOM standard set to the Spanish setting pave the way to standardize the collection of variables in LC.

Detection of selective cationic amphipatic antibacterial peptides by Hidden Markov models.

Antibacterial peptides are researched mainly for the potential benefit they have in a variety of socially relevant diseases, used by the host to protect itself from different types of pathogenic bacteria. We used the mathematical-computational method known as Hidden Markov models (HMMs) in targeting a subset of antibacterial peptides named Selective Cationic Amphipatic Antibacterial Peptides (SCAAPs). The main difference in the implementation of HMMs was focused on the detection of SCAAP using principally five physical-chemical properties for each candidate SCAAPs, instead of using the statistical information about the amino acids which form a peptide. By this method a cluster of antibacterial peptides was detected and as a result the following were found: 9 SCAAPs, 6 synthetic antibacterial peptides that belong to a subregion of Cecropin A and Magainin 2, and 19 peptides from the Cecropin A family. A scoring function was developed using HMMs as its core, uniquely employing information accessible from the databases.

Maximization of thermal conductance at interfaces via exponentially mass-graded interlayers.

We propose a strategy to potentially best enhance interfacial thermal transport through solid-solid interfaces by adding nano-engineered, exponentially mass-graded intermediate layers. This exponential design rule results in a greater enhancement than a linearly mass-graded interface. By combining calculations using non-equilibrium Green's functions (NEGF) and non-equilibrium molecular dynamics (NEMD), we investigated the role of impedance matching and anharmonicity in the enhancement in addition to geometric parameters such as the number of layers and the junction thickness. Our analysis shows that the effect on thermal conductance is dominated by the phonon thermalization through anharmonic effects, while elastic phonon transmission and impedance matching play a secondary role. In the harmonic limit, increasing the number of layers results in greater elastic phonon transmission at each individual boundary, countered by the decrease of available conducting channels. Consequently, conductance initially increases with number of layers due to improved bridging, but quickly saturates. The presence of slight anharmonic effects (at very low temperature, T = 2 K) turns the saturation into a monotonically increasing trend. Anharmonic effects can further facilitate interfacial thermal transport through the thermalization of phonons at moderate temperatures. At high temperature, however, the role of anharmonicity as a facilitator of interfacial thermal transport reverses. Strong anharmonicity introduces significant intrinsic resistance, overruling the enhancement in thermal conduction at the boundaries. It follows that at a particular temperature, there exists a corresponding junction thickness at which thermal conductance is maximized.

Bioinformatics characterisation of the (mutated) proteins related to Andersen-Tawil syndrome.

In the last two decades, a group of proteins whose mutations are associated with a disease manifested by episodes of muscle weakness (periodic paralysis), changes in heart rhythm (arrhythmia), and developmental abnormalities has been under constant study. This malady is known as Andersen-Tawil syndrome, with ~60% of cases of this syndrome being caused by 16 mutations in the KCNJ2 gene [UniProt ID: P63252-01-P63252-17]. In this work, we present a computational study designed to obtain a fingerprint of Andersen-Tawil mutated proteins and differentiate them from mutated proteins associated with Brugada syndrome and from functional groups of proteins belonging to APD3, UniProt, and CPPsite databases. We show here that Andersen-Tawil mutated proteins are characterized by specific features that can be used to differentiate, with a high level of certainty (90%), proteins carrying these mutations from similar functional groups, such as mutated proteins associated with Brugada syndrome, and from different functional protein and peptide groups, such as antimicrobial peptides, Cell-Penetrating Peptides, and intrinsically disorder proteins. Therefore, our main results allow us to conjecture that it is possible to identify the group of the Andersen-Tawil mutated proteins by their "PIM profile". Furthermore, when we applied this "fingerprint PIM profile" on the UniProt database, we observed that one protein found in humans [UniProt ID: Q9NZV8], and six of all "reviewed" proteins found in living organisms, possess a very similar PIM profile as the Andersen-Tawil mutated protein group. The bioinformatics "fingerprint" of the Andersen-Tawil mutated proteins was retrieved using the in-house bioinformatics system named Polarity Index Method® and supported-at residues level- by the algorithms for the prediction of intrinsic disorder predisposition, such as PONDR® FIT, PONDR® VLXT, PONDR® VSL2, PONDR® VL3, FoldIndex, IUPred, and TopIDP.

Construction of a high-density interspecific (Lens culinaris x L. odemensis) genetic map based on functional markers for mapping morphological and agronomical traits, and QTLs affecting resistance to Ascochyta in lentil.

Usage of high-throughput sequencing approaches allow for the generation and characterization of reference transcriptome datasets that support gene-based marker discovery, which in turn can be used to build genetic maps among other purposes. We have obtained a transcriptome assembly including 49,453 genes for the lentil (Lens culinaris Medik.) cultivar Alpo using RNAseq methodology. This transcriptome was used as reference to obtain 6,306 quality polymorphic markers (SNPs and short indels) analyzing genotype data from a RIL population at F7 generation derived from the interspecific cross between L. culinaris cv. Alpo and L. odemensis accession ILWL235. L. odemensis is a wild species included in the secondary gene pool and can be used as a source for gene introgression in lentil breeding programs. Marker data were used to construct the first genetic interspecific map between these two species. This linkage map has been used to precisely identify regions of the CDC-Redberry lentil draft genome in which the candidate genes for some qualitative traits (seed coat spotting pattern, flower color, and stem pigmentation) could be located. The genome regions corresponding to a significant single quantitative trait locus (QTL) controlling "time to flowering" located in chromosome 6 and three QTLs regulating seed size and positioned in chromosomes 1 and 5 (two QTLs) were also identified. Significant QTLs for Ascochyta blight resistance in lentil were mapped to chromosome 6 in the genome region or close to it where QTLs for Ascochyta blight resistance have previously been reported.

A genome-wide identification and comparative analysis of the lentil MLO genes.

Powdery mildew is a widespread fungal plant disease that can cause significant losses in many crops. Some MLO genes (Mildew resistance locus O) have proved to confer a durable resistance to powdery mildew in several species. Resistance granted by the MLO gene family members has prompted an increasing interest in characterizing these genes and implementing their use in plant breeding. Lentil (Lens culinaris Medik.) is a widely grown food legume almost exclusively consumed as dry seed with an average world production of 4.5 million tons. Powdery mildew causes severe losses on certain lentil cultivars under particular environmental conditions. Data mining of the lentil CDC Redberry draft genome allowed to identify up to 15 gene sequences with homology to known MLO genes, designated as LcMLOs. Further characterization of these gene sequences and their deduced protein sequences demonstrated conformity with key MLO protein characteristics such as the presence of transmembrane and calmodulin binding domains, as well as that of other conserved motifs. Phylogenetic and other comparative analyses revealed that LcMLO1 and LcMLO3 are the most likely gene orthologs related to powdery mildew response in other species, sharing a high similarity with other known resistance genes of dicot species, such as pea PsMLO1 and Medicago truncatula MtMLO1 and MtMLO3. Sets of primers were designed as tools to PCR amplify the genomic sequences of LcMLO1 and LcMLO3, also to screen lentil germplasm in search of resistance mutants. Primers were used to obtain the complete sequences of these two genes in all of the six wild lentil relatives. Respective to each gene, all Lens sequences shared a high similarity. Likewise, we used these primers to screen a working collection of 58 cultivated and 23 wild lentil accessions in search of length polymorphisms present in these two genes. All these data widen the insights on this gene family and can be useful for breeding programs in lentil and close related species.