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One of the molecular hallmarks of amyloidoses is ordered protein aggregation involving the initial formation of soluble protein oligomers that eventually grow into insoluble fibrils. The identification and characterization of molecular species critical for amyloid fibril formation and disease development have been the focus of intense analysis in the literature. Here, using photo-induced cross-linking of unmodified proteins (PICUP), we studied the early stages of oligomerization of human transthyretin (TTR), a plasma protein involved in amyloid diseases (ATTR amyloidosis) with multiple clinical manifestations. Upon comparison, the oligomerization processes of wild-type TTR (TTRwt) and several TTR variants (TTRV30M, TTRL55P, and TTRT119M) clearly show distinct oligomerization kinetics for the amyloidogenic variants but a similar oligomerization mechanism. The oligomerization kinetics of the TTR amyloidogenic variants under analysis showed a good correlation with their amyloidogenic potential, with the most amyloidogenic variants aggregating faster (TTRL55P > TTRV30M > TTRwt). Moreover, the early stage oligomerization mechanism for these variants involves stepwise addition of monomeric units to the growing oligomer. A completely different behavior was observed for the nonamyloidogenic TTRT119M variant, which does not form oligomers in the same acidic conditions and even for longer incubation times. Thorough characterization of the initial steps of TTR oligomerization is critical for better understanding the origin of ATTR cytotoxicity and developing novel therapeutic strategies for the treatment of ATTR amyloidosis. info:eu-repo/semantics/publishedVersion

Edible wild plants are part of the ethnobotanical and gastronomic heritage of different geographical areas. Corema album (L.) D. Don is an endemic species of the dune systems of the Atlantic coast of the Iberian Peninsula. The aerial parts of Corema album are a source of nutrients and antioxidants. The Corema album white berry (Portuguese crowberry) is rich in calcium, iron, and zinc. The plant also shows high phenolic content and antioxidant capacity associated with the leaves, fruit, and flowers. The presence of organic acids, namely phenolic acids, such as hydroxycinnamic acids, and long chain polyunsaturated fatty acids (PUFAs) omega-3 and omega-6 has also been confirmed. Toxicity studies evaluated by cell viability tests with human intestinal epithelium model cells (Caco-2) have shown that, at low concentrations, plant extracts may present beneficial effects. info:eu-repo/semantics/publishedVersion

The functional composition of plant communities in montane regions has been studied for decades, and most recent analyses find that environmentally favourable landscapes at lower altitudes tend to be dominated by species with resource-acquisitive traits, while more resource-conservative taxa dominate higher-altitude communities. However, it is unclear the extent to which this pattern is driven by co-gradient variation within clades or changes in clade representation across the gradient. To test for co-gradient variation, species composition, phylogenetic structure and functional traits were quantified for 97 species within the plant family Melastomataceae at five locations across a 2500- m altitudinal gradient along Volcán Barva in Costa Rica. Average melastome leaf force to punch, specific leaf area and leaf size vary with altitude, while four other functional traits do not. Taxonomic dissimilarity between communities was correlated with altitudinal difference, while phylogenetic dissimilarity was correlated with altitudinal dissimilarity only when measured with a metric that emphasizes shallow turnover of the tips of the phylogeny. These results highlight how species turnover may be more pronounced than functional or phylogenetic variation along altitudinal gradients. In addition, these results highlight the conservation value of lowland tropical forests, which here harbour a disproportionate amount of phylogenetic and functional diversity La composición funcional de las comunidades de plantas en las regiones montañosas se ha estudiado durante décadas, y los análisis más recientes encuentran que los paisajes ambientalmente favorables en altitudes más bajas tienden a estar dominados por especies con características de adquisición de recursos, mientras que los taxones más conservadores de recursos dominan las comunidades de altitudes más altas. . Sin embargo, no está claro hasta qué punto este patrón es impulsado por la variación del cogradiente dentro de los clados o los cambios en la representación de los clados a lo largo del gradiente. Para evaluar la variación del cogradiente, se cuantificaron la composición de especies, la estructura filogenética y los rasgos funcionales de 97 especies dentro de la familia de plantas Melastomataceae en cinco lugares a lo largo de un gradiente altitudinal de 2500 m a lo largo del Volcán Barva en Costa Rica. La fuerza promedio de la hoja de melastoma para perforar, el área foliar específica y el tamaño de la hoja varían con la altitud, mientras que otros cuatro rasgos funcionales no lo hacen. La disimilitud taxonómica entre comunidades se correlacionó con la diferencia altitudinal, mientras que la disimilitud filogenética se correlacionó con la disimilitud altitudinal solo cuando se midió con una métrica que enfatiza la rotación superficial de las puntas de la filogenia. Estos resultados resaltan cómo el recambio de especies puede ser más pronunciado que la variación funcional o filogenética a lo largo de los gradientes altitudinales. Además, estos resultados resaltan el valor de conservación de los bosques tropicales de tierras bajas, que aquí albergan una cantidad desproporcionada de diversidad filogenética y funcional. Universidad Nacional, Costa Rica Escuela de Ciencias Biológicas

Background:Anti-Dense Fine Speckled 70 (DFS70), also known as lens epithelium-derived growth factor (LEDGF) is a common finding when ANA are positive (1.7% in the whole population and 4.6% in the ANA-positive samples). DFS70 antibodies are rare in SARD, especially in the absence of clinical evidence or concomitant anti-extractable nuclear antigen (ENA) antibodies.Objectives:Our study aimed to understand the meaning of anti-DFS70 antibodies and characterize the clinical and serological features of patients with anti-DFS70 positivity.Methods:We performed a retrospective observational study of consecutive patients followed up at 9 Portuguese Rheumatology Centres observed from January 2018 until April of 2020 with anti-DFS70 antibodies positivity. Descriptive statistics were presented as mean ± standard deviation if normally distributed or as median and interquartile range if non-normally distributed (continuous variables) or as absolute and relative frequencies (categorical variables). Sensibility and specificity were calculated. Positive and negative predictive values were calculated between patients with and without SARD-specific autoantibodies. Associations between DFS70 with other disease-specific antibody and clinical manifestations were tested using Chi-Square or Fischer’s Exact Test, as appropriate.Results:120 patients were included, 99 (82.5%) were female with a mean age of 47.8 ± 18.2 years. 96.7% of the patients had ANA titters ≥1:160 (32.5% 1:160; 38.3% 1:320; 16.7% 1:640; 7.5% 1:1280 and 1.7% 1:2560) and 3.3% ANA The main clinical reasons for ANA determination was arthralgia (44.2%), arthritis (11.6%) and Raynaud Phenomenon (RP) (10%). The main analytical reason (7.5%) was an elevation of inflammatory parameters (C-Reactive Protein (CRP) or Erythrocyte Sedimentation Rate (ESR), leukopenia (3.3%) and anaemia (2.5%). Concerning the immunology: 58.3% of patients didn´t have an associated antibody, 9.2% had a positive rheumatoid factor, 5.8% positive ds-DNA, 4.2% histone and 3.3% SS-A. 26 patients had more than one associated antibody.30 (25%) patients were healthy; 43 (35.8%) patients had Systemic Autoimmune Rheumatic Diseases (SARD) and 47 patients (39.2%) had other diseases (non-SARD). Among patients with a SARD, 16 patients presented an isolated positive anti-DFS70 and 27 patients had other antibodies associated. There was found a positive association with non-SARD and arthralgia (p=0.001) and SARD with arthritis (pThe sensitivity of isolated DFS70 was 70.1% and specificity was 62.8%. The positive predictive value was 77.1% and the negative predictive value was 54.0%.Table 1.Comparative analysis using chi-square or Fischer testSARDNon-SARDp-valueArthralgia, n10430.001Arthritis, n140Raynaud Phenomenon, n750.114Raised Inflammation parameters, n630.045Anaemia, n121.000Leukopenia, n310.131Conclusion:We concluded that 64.2% of patients with positive DFS70 did not present a SARD and if we only consider patients with isolated anti-DFS70, 77.1% didn´t present a SARD. Therefore, in our study, 22.9% of the patients presented a SARD, which was associated with some clinical features like arthritis or raised inflammatory parameters (pReferences:[1]Leuchten, N. et al. Performance of Antinuclear Antibodies for Classifying Systemic Lupus Erythematosus: A systematic literature review and meta-regression of diagnostic data. Arthritis Care Res. 70, 428–438 (2018).[2]Carter JB, Carter S, Saschenbrecker S, Goeckeritz BE (2018) Recognition and relevance of anti-DFS70 autoantibodies in routine antinuclear autoantibodies testing at a community hospital.Disclosure of Interests:None declared

Here we document for the first time the presence of invasive lionfish larvae (Pterois volitans) in the Gulf of Mexico. Three lionfish larvae (standard length: 3.9–5.9 mm) were collected during summer ichthyoplankton surveys in the northern Gulf of Mexico in 2011, with species identification confirmed through the genetic analysis of mitochondrial DNA. Pigmentation patterns of these larvae are described and compared with published lionfish descriptions. Otolith microstructure analysis revealed that larvae were 14–17 days old and that spawning occurred in June and July. A biophysical dispersal model was used to backtrack larvae to their potential spawning locations and results indicated that spawning occurred in the southern Gulf of Mexico near the Yucatan Peninsula, suggesting that these larvae may have been transported into the northern Gulf of Mexico by the Loop Current. Here we provide useful information for identifying lionfish larvae and offer insight into lionfish spawning and larval dispersal pathways.

Introduction: Rapid tests represent an important diagnostic tool, providing results in a short period of time and eliminating the use of large automated equipment. Objective: To evaluate the performance of five rapid test kits for troponin I detection in serum. Materials and methods: Samples from 100 patients with suspected acute myocardial infarction (AMI) were selected from a hospital in Barbacena, MG, Brazil. They were tested in the five troponin I commercial rapid test kits and the results were compared with the study reference method (quantitative chemiluminescent immunoassay). Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and correlation coefficients of the rapid tests against the reference method were defined. Results: The kits from Abon®, Interteck®, Medtest® and Wama® presented the same performance, reaching equal levels of sensitivity (98.08%), specificity (100%), PPV (100%), NPV (97.96%), and correlation coefficient (0.99). The Eco Diagnostica® kit presented lower sensitivity (82.69%), low correlation coefficient (0.91) and NPV (84.21%), not reaching ideal levels even though lying within the confidence interval. Discussion: The results obtained with the Abon®, Interteck®, Medtest® and Wama® test kits corroborate pre-existing literature data on the diagnostic accuracy of rapid tests for troponin detection. These tests are allowed for immediate decision making by physicians and can be used to reduce unnecessary hospitalization time and costs associated with a suspected AMI. Conclusion: The kits from Abon®, Interteck®, Medtest® and Wama® showed excellent diagnostic performance, what makes them an important diagnostic tool in smaller laboratories without automated equipment. RESUMEN Introducción: Hoy en día, las pruebas rápidas representan importante herramienta diagnóstica, ofrecen resultados en corto espacio de tempo y dispensan el uso de equipos automatizados. Objetivo: Evaluar el desempeño de cinco kits de pruebas rápidas para detectar troponina I en suero. Material y métodos: Se eligieron 100 especímenes de pacientes sospechosos de infarto agudo de miocardio (IAM) de un hospital en el municipio de Barbacena, Minas Gerais, Brasil. Los especímenes fueron testados en los cinco kits comerciales de prueba rápida de troponina I y el resultado se comparó con el método considerado referencia en el estudio (inmunoensayo quimioluminiscente cuantitativo). Luego, se establecieron los niveles de sensibilidad, especificidad, valor predictivo positivo (VPP), valor predictivo negativo (VPN) y coeficiente de correlación de las pruebas rápidas con respecto al método de referencia. Resultados: Las marcas Abon®, Interteck®, Medtest® y Wama® tuvieron el mismo desempeño, alcanzando niveles iguales de sensibilidad (98,08%), especificidad (100%), VPP (100%), VPN (97,96%) y coeficiente de correlación (0,99), mientras la marca Eco Diagnóstica® presentó 82,69% de sensibilidad, 0,91 de coeficiente de correlación y 84,21% de VPN, no alcanzando los niveles ideales, aunque dentro del intervalo de confianza. Discusión: Los resultados obtenidos con las marcas Abon®, Interteck®, Medtest® e Wama® confirman datos preexistentes en la literatura sobre la precisión diagnóstica de las pruebas rápidas para detectar troponina. Esas pruebas permiten a los médicos adoptar decisiones de forma inmediata y pueden ser usados para reducir tiempo y costos de internaciones innecesarias cuando hay sospecha de IAM. Conclusión: Las marcas Abon®, Interteck®, Medtest® e Wama® presentaron excelente desempeño diagnóstico y representan importante herramienta diagnóstica en laboratorios menores, sin equipos automatizados. RESUMO Introdução: Atualmente, os testes rápidos representam importante ferramenta diagnóstica, fornecendo resultados em curto espaço de tempo e dispensando a utilização de grandes automações. Objetivo: Avaliar o desempenho de cinco kits de testes rápidos para pesquisa sérica de troponina I. Materiais e métodos: Foram selecionadas 100 amostras de pacientes com suspeita de infarto agudo do miocárdio (IAM) de um hospital do município de Barbacena, Minas Gerais, Brasil. As amostras foram testadas nos cinco kits comerciais de teste rápido de troponina I e o resultado foi comparado com o método considerado referência no estudo (imunoensaio quimioluminescente quantitativo). Em seguida, foram definidos níveis de sensibilidade, especificidade, valor preditivo positivo (VPP), valor preditivo negativo (VPN) e coeficiente de correlação dos testes rápidos em relação ao método de referência. Resultados: Os kits Abon®, Interteck®, Medtest® e Wama® apresentaram o mesmo desempenho, atingindo níveis iguais de sensibilidade (98,08%), especificidade (100%), VPP (100%), VPN (97,96%) e coeficiente de correlação (0,99). O kit Eco Diagnóstica® apresentou 82,69% de sensibilidade, 0,91 de coeficiente de correlação e 84,21% de VPN, não atingindo os níveis ideais, mesmo dentro do intervalo de confiança. Discussão: Os resultados obtidos com os kits Abon®, Interteck®, Medtest® e Wama® confirmam dados preexistentes na literatura sobre a exatidão diagnóstica dos testes rápidos para detecção de troponina. Esses testes permitem a tomada de decisão imediata pelo médico e podem ser usados para reduzir tempo e custos de internações desnecessárias na suspeita de IAM. Conclusão: Os kits Abon®, Interteck®, Medtest® e Wama® apresentaram excelente desempenho diagnóstico e constituem importante ferramenta diagnóstica em laboratórios menores, sem equipamentos automatizados.

Mesophotic coral reef ecosystems are remote from coastal stressors, but are still vulnerable to over-exploitation, and remain mostly unprotected. They may be the key to coral reefs resilience, yet little is known about the pattern of larval subsidies from deeper to shallower coral reef habitats. Here we use a biophysical modeling approach to test the hypothesis that fishes from mesophotic coral reef ecosystems may replenish shallow reef populations. We aim at identifying the spatio-temporal patterns and underlying mechanisms of larval connections between Pulley Ridge, a mesophotic reef in the Gulf of Mexico hosting of a variety of shallow-water tropical fishes, and the Florida Keys reefs. A new three-dimensional (3D) polygon habitat module is developed for the open-source Connectivity Modeling System to simulate larval movement behavior of the bicolor damselfish, Stegastes partitus, in a realistic 3D representation of the coral reef habitat. Biological traits such as spawning periodicity, mortality, and vertical migration are also incorporated in the model. Virtual damselfish larvae are released daily from the Pulley Ridge at 80 m depth over 60 lunar spawning cycles and tracked until settlement within a fine resolution (~900 m) hydrodynamic model of the region. Such probabilistic simulations reveal mesophotic-shallow connections with large, yet sporadic pulses of larvae settling in the Florida Keys. Modal and spectral analyses on the spawning time of successful larvae, and on the position of the Florida Current front with respect to Pulley Ridge, demonstrate that specific physical-biological interactions modulate these “perfect storm” events. Indeed, the co-occurrence of (1) peak spawning with frontal features, and (2) cyclonic eddies with ontogenetic vertical migration, contribute to high settlement in the Florida Keys. This study demonstrates that mesophotic coral reef ecosystems can also serve as refugia for coral reef fish and suggests that they have a critical role in the resilience of shallow reef communities.

Pulley Ridge is a limestone ridge that extends nearly 300 km along the southwestern Florida shelf in the eastern Gulf of Mexico. The southern terminus of Pulley Ridge supports a mesophotic coral ecosystem (MCE) at depths of 59–105 m and is the deepest known photosynthetic coral reef off the continental United States. The biodiversity consists of 95 species of macroalgae, 92 demosponges, 18 octocorals, 17 scleractinian corals, 9 antipatharian corals, and 86 fishes. Twenty managed fishery species occur at Pulley Ridge including red grouper, and since 2010 the lionfish population has dramatically increased. The dominant scleractinian corals are plate like corals of the family Agariciidae (Agaricia spp. and Helioseris cucullata), Montastraea cavernosa, Madracis spp., and Oculina diffusa. The percent cover of benthic biota averaged 49.9% over all regions of Pulley Ridge, and macroalgae were dominant (46.5% cover). Scleractinian corals averaged 1.5% cover and sponges had 1.2% cover. In the past 10 years, the Pulley Ridge MCE had a substantial loss of scleractinian coral. The percent coral cover on the Main Ridge dropped from 12.8% in 2003 to 0.9% by 2012–2015, a 93% loss of coral. However, recent surveys show the majority of corals to be relatively healthy; only 1.21% of the colonies counted (38,368) showed signs consistent with “white syndromes” disease. The prevalence of disease on Pulley Ridge is relatively low compared to the Caribbean. The factors causing the decline of the coral communities at Pulley Ridge between 2003 and 2012 are unknown.

Many riverboats are equipped with a submerged engine exhaust, which releases combustion gases directly into the water body. The water quality associated to a typical riverboat discharge used in Brazilian Amazon was evaluated. Polycyclic aromatic hydrocarbons (PAHs) associated with fuel combustion are priority control pollutants as they can have an impact on human health and biota. Water samples were assessed for physical and chemical parameters, acute toxicity to the aquatic organism Daphnia magna (Cladocera, Daphniidae), PAH concentration, and total equivalent toxicity (BaPeq). The tests were performed with D500 diesel (500 ppm sulfur), which is traditionally used in combustion systems, and blends of diesel/butanol up to 25 % (v/v). PAH concentration was reduced by 31 % by replacing pure diesel (290.78 μg L−1) with 25 % diesel/butanol (201.05 μg L−1). Butanol was responsible for lowering the BaPeq (≤ 34 %), and accordingly the lethality of the bioindicator (EC50 0.10 to 0.46 %).

One of the main challenges facing the development of effective anti HIV-1 medicines relates to the high mutation rate of essential enzymes, such as HIV-1 Protease (HIV1Pr).[1] Pereira Vaz et al. [2] first reported a threonine insertion at position 35 (E35E_T), in the HIV1Pr coding region, among treatment-naive subtype C infected individuals. Undetectable viral loads were attained after antiretroviral therapy in such individuals, with no associated major mutations, implying null contribution of E35E_T to viral resistance. Interestingly, a new study suggests a potential additive effect of position 35 insertions when in presence of major mutations – ultimately leading to resistance to HIV1Pr inhibitors in higher extent. [3] In order to study the role of the E35E_T insertion in the structure and ligand-binding propensity of HIV1Pr, homology models were generated from subtype B and subtype C base sequences, using available X-ray structures corresponding to highest identity sequences as template. Fifty (50)-nanoseconds Molecular Dynamics (MD) simulations were then performed for unbound and bound (HIV1PR:darunavir complex) structures of the wild-type form and a single‑point major mutation variant of HIV1PR – in all cases in presence and absence of E35_T. Combining simple measurements like the root mean square (RMS) deviations and fluctuations, applied to the whole protein and to its two functional flap regions, with principal component analysis (PCA) of the multiple MD trajectories, we herein contrast the behaviour of all systems in attempt to dissect the putative role of E35E_T in the resistance towards HIV1PR inhibitors.

Whether mesophotic reefs will behave as refugia for corals threatened by global climate change and coastal development depends on vertical exchange of larvae between diverse habitats. Here we use a biophysical model of larval dispersal to estimate vertical connectivity of a broadcasting (Orbicella faveolata) and a brooding (Porites astreoides) species of coral in the US Virgin Islands. Modeling predicts subsidy to shallow areas by mesophotic larvae of both species based on local hydrology, adult reproductive characteristics, larval traits, and a wide range of scenarios developed to test depth-sensitive factors, such as fertilization rates and post-settlement survivorship. In extreme model scenarios of reduced fertilization and post-settlement survivorship of mesophotic larvae, 1–10 % local mesophotic subsidy to shallow recruitment is predicted for both species, which are demographically significant. Although direct vertical connectivity is higher for the broadcaster, the brooder demonstrates higher local multigenerational vertical connectivity, which suggests that local P. astreoides populations are more resilient than those of O. faveolata, and corroborates field studies. As shallow habitat degrades, mesophotic–shallow subsidy is predicted to increase for both species. This study is the first of its kind to simulate larval dispersal and settlement between habitats of different depths, and these findings have local, regional, and global implications for predicting and managing coral reef persistence in a changing climate.

Grain legumes are a vital source of inexpensive plant-based proteins and amino acids and, eaten as part of a healthy diet, they help to prevent chronic diseases. Potential health benefits of grain legumes have been mainly attributed to the presence of secondary metabolites with antioxidant activity. Breeding for improved end-user’s quality is a complex task due to trait interaction. Some of these metabolites, such as phenolic compounds, that act as health-promoting agents are also considered antinutrients, influencing both taste and consumers’ acceptability. Under the scope of LEGATO and BEGEQA projects, we studied the genetic architecture of the total phenolic compounds content in grass pea and common bean seeds. Association mapping approaches were applied to both common bean and grass pea germplasm collections and the genomic regions controlling these bioactive compounds concentration were identified. This work will contribute to the development of grain legume varieties with better nutritional quality, meeting consumers’ expectations at the same time that support the improvement and production of a plant resource with a vital role in sustainable agriculture.

Previous studies have reported promising differences in the quality of kernels from farmers' maize populations collected in a Portuguese region known to produce maize-based bread. However, several limitations have been identified in the previous characterizations of those populations, such as a limited set of quality traits accessed and a missing accurate agronomic performance evaluation. The objectives of this study were to perform a more detailed quality characterization of Portuguese farmers' maize populations ; to estimate their agronomic performance in a broader range of environments ; and to integrate quality, agronomic, and molecular data in the setting up of decision-making tools for the establishment of a quality-oriented participatory maize breeding program. Sixteen farmers' maize populations, together with 10 other maize populations chosen for comparison purposes, were multiplied in a common-garden experiment for quality evaluation. Flour obtained from each population was used to study kernel composition (protein, fat, fiber), flour's pasting behavior, and bioactive compound levels (carotenoids, tocopherols, phenolic compounds). These maize populations were evaluated for grain yield and ear weight in nine locations across Portugal ; the populations' adaptability and stability were evaluated using additive main effects and multiplication interaction (AMMI) model analysis. The phenotypic characterization of each population was complemented with a molecular characterization, in which 30 individuals per population were genotyped with 20 microsatellites. Almost all farmers' populations were clustered into the same quality-group characterized by high levels of protein and fiber, low levels of carotenoids, volatile aldehydes, α- and δ-tocopherols, and breakdown viscosity. Within this quality-group, variability on particular quality traits (color and some bioactive compounds) could still be found. Regarding the agronomic performance, farmers' maize populations had low, but considerably stable, grain yields across the tested environments. As for their genetic diversity, each farmers' population was genetically heterogeneous ; nonetheless, all farmers' populations were distinct from each other's. In conclusion, and taking into consideration different quality improvement objectives, the integration of the data generated within this study allowed the outline and exploration of alternative directions for future breeding activities. As a consequence, more informed choices will optimize the use of the resources available and improve the efficiency of participatory breeding activities.

Over the last 30 years, HIV has grown to a pandemic status with more than 36 million people infected worldwide. Current therapies provide a significant improvement in the quality of patients’ lives, specifically the Highly Active Anti-Retroviral Therapy (HAART). Yet, viral resistance development towards anti-HIV medication stands as the main obstacle to an effective therapy, having also a substantial economic impact on healthcare systems worldwide. Such viral resistance is primarily related to mutations occurring mainly on the active site of viral key enzymes, capable of decreasing the pocket’s capability to establish the necessary non-covalent interactions with the drugs. Even so, mutations outside the enzyme’s active site can also lead to resistances, by causing changes on its structure and/or chemical environment. Among the two HIV virus types, HIV-1 stands as the most studied and prominent, with HIV‑1 protease being one of the main viral targets for therapy.[1] Given the ease of quickly and affordably sequence HIV from infected individuals, considerable progress – in the sense of predicting resistance towards drugs – could be made by developing tools to link specific genetic mutations with the resulting structural and chemical alterations in the active site of the target enzymes.[2] In recognition of a serious medical need identified by a team of virologists working at the University of Coimbra teaching Hospital and with the intent of helping rationalize and personalize the choice of anti-HIV therapies, we set out to develop a new computational algorithm to predict resistance to protease inhibitors in HIV‑1 via detection of binding-site Molecular Interactions Field (MIF) dissimilarities. Briefly, the algorithm works by 1) automatically generating high-quality 3D protein model structures from HIV‑1 protease sequences; 2) capturing subtle, mutation-induced, chemical perturbations within the binding sites of resistant and non-resistant HIV‑1 protease structures using a MIF-based approach; and 3) quantifying binding site dissimilarities based on MIF analysis, and translating these into a resistance score. In terms of its predictive power, preliminary testing of the algorithm using several different HIV protease sequences showed promising levels of sensitivity and specificity. Despite both sequence- and structure-based computational approaches to the prediction of HIV drug resistance have been proposed in the past, our present work stands out from other known algorithms as a first implementation of a fast structure-based algorithm capable of discriminating between HIV sequences that may be susceptible or resistant to commercially available protease inhibitors. Since the problem of mutation-induced resistance cuts across virtually all pathogenic virus, we believe that our approach may be extended to a wide range of viral targets besides HIV-1. References: Baxter D. J.; Chasanov M. W.; Adams L. J. J AIDS Clin Res. 2016, 7, 581. Weber I.; Kneller D.; Wong-Sam A.; Future Med Chem., 2015, 7(8), 1023-1038.

Common bean (Phaseolus vulgaris L.) is among the most important grain legumes for human consumption worldwide. Portugal has a potentially promising common bean germplasm, resulting from more than five centuries of natural adaptation and farmers' selection. Nevertheless, limited characterization of this resource hampers its exploitation by breeding programs. To support a more efficient conservation of the national bean germplasm and promote its use in crop improvement, we performed, for the first time, a simultaneous molecular marker (21 microsatellites and a DNA marker for phaseolin-type diversity analysis) and seed and plant morphological characterization (14 traits) of 175 accessions from Portuguese mainland and islands traditional bean-growing regions. A total of 188 different alleles were identified and an average pairwise Cavalli-Sforza and Edwards' chord genetic distance of 0.193 was estimated among accessions. To relate the Portuguese germplasm with the global common bean diversity, 17 wild relatives and representative accessions from the Andean and Mesoamerican gene pools were evaluated at the molecular level. No correlation was detected between the variability found and the geographic origin of accessions. Structure analysis divided the collection into three main clusters. Most of the Portuguese accessions grouped with the race representatives and wild relatives from the Andean region. One third of the national germplasm had admixed genetic origin and might represent putative hybrids among gene pools from the two original centers of domestication in the Andes and Mesoamerica. The molecular marker-based classification was largely congruent with the three most frequent phaseolin haplotype patterns observed in the accessions analyzed. Seed and plant morphological characterization of 150 Portuguese common bean accessions revealed a clear separation among genetic structure and phaseolin haplotype groups of accessions, with seed size and shape and the number of locules per pod the most discriminant traits. Additionally, we used molecular and morphological data to develop a series of smaller core collections that, by maximizing the genetic and morphological diversity of the original collection, represents the Portuguese common bean germplasm with minimum repetitiveness. A core collection with 37 accessions contained 100% of the genetic variation found in the entire collection. This core collection is appropriate for a more detailed characterization and should be explored, as a priority, in national and international common bean breeding efforts. Furthermore, the identified intermediate accessions (with admixed genetic origin) may have novel genetic combinations useful in future bean breeding.

INTRODUCTION The workflow in clinical flow cytometry laboratories must constantly be reviewed to develop technical procedures that improve quality and productivity and reduce costs. Using the Beckman Coulter dry coating technology, we customized a ten-color tube with dried antibody reagents, designated the Duraclone screening tube (DST), for screening hematological malignancies. Here, we compared the applicability, clinical and numerical equivalence, and cost and time required for the technical procedures between the liquid reagents and the DST. METHODS The DST contains CD4 + Kappa-FITC, CD8 + Lambda-PE, CD3 + CD14-ECD, CD33-PE-Cy5.5, CD20 + CD56-PE-Cy7, CD34-APC, CD19-APC-AlexaFluor700, CD10-APC-AlexaFluor750, CD5-Pacific Blue, and CD45-Krome Orange. We evaluated 20 bone marrow samples, 13 peripheral blood samples, 6 lymph node biopsy samples, 5 fine-needle aspirate samples, 5 cerebrospinal fluid samples, and 1 pleural fluid sample. RESULTS The DST was useful for more than 60% of our samples. It was able to enumerate the majority of the populations in all types of samples with a statistically acceptable correlation with the liquid reagents. The use of the DST translated into significant time and cost savings of 15.8% and 12.3%, respectively, compared with the use of the liquid reagent. The cost was reduced by $14.36 per sample. CONCLUSIONS The DST is an efficient solution for screening hematological malignancies with improved quality, productivity, standardization, and sustainability. These improvements could benefit patients by providing faster diagnoses using a higher quality and lower cost reagent.

A 3-year ecological study of small mammals was carried out in an endemic area for hantavirus pulmonary syndrome in the state of Santa Catarina in Southern Brazil. A total of 994 rodents of 14 different species corresponding to the subfamilies of Sigmodontinae, Murinae, Eumysopinae, and Caviinae were captured during 2004–2006. Oligoryzomys nigripes and Akodon montensis were the most abundant species and showed a clear seasonal pattern with higher population sizes during the winter. Rodent population outbreaks, associated within bamboo mast seeding events, were detected predominantly in areas where hantavirus pulmonary syndrome cases were notified in the state. Antibody reactivity to Hantavirus was detected in five sigmodontine species: O. nigripes (39/435), A. montensis (15/318), Akodon paranaensis (4/37), Thaptomys nigrita (1/86) and Sooretamys angouya (1/12). The highest hantavirus antibody prevalence occurred during the period of highest population size in A. montensis. For O. nigripes, hantavirus prevalence was higher in late spring, when reproduction was more frequent. Co-circulation of Juquitiba (JUQV) and Jabora (JABV) viruses was observed – JABV in A. paranaensis and A. montensis; JUQV in O. nigripes and T. nigrita. JABV occurrence was associated to gender and population size of the rodent while JUQV was related to gender, season, temperature, and locality.

This is one of the few studies on food habits of armadillos and anteaters in the Caatinga, Brazil. Our aim was to describe food items found in fecal and stomach samples of six species (Dasypus novemcinctus, D. septemcinctus, Euphractus sexcinctus, Myrmecophaga tridactyla, Tamandua tetradactyla, Tolypeutes tricinctus) at the Serra da Capivara National Park, Piaui State, Brazil. For most species, invertebrates — especially Isoptera and Hymenoptera — were the main food source. Seeds were found in samples of most species studied, including M. tridactyla and T. tetradactyla.

Sodium alginate films with aloe vera extract were prepared by the casting/solvent evaporation technique. The resulting films were characterized by differential scanning calorimetry, Fourier transform-infrared spectroscopy, scanning electron microscopy, and mechanical and water absorption tests. The in vitro degradation of the films was also investigated over 14 days. Results show that aloe vera contributes to both enhancing the thermal and mechanical properties of the films and decreasing the weight loss during in vitro degradation.

Lathyrus sativus has high potential both as food and fodder crop but can be severely infected by rust. This study assessed the resistance level of a collection of L. sativus accessions against three rust species (Uromyces pisi, U. ciceris-arietini and U. viciae-fabae) and characterized, for the first time, macro and microscopically the resistance to U. pisi. All L. sativus accessions were highly resistant to U. ciceris-arietini and to U. viciae-fabae but showed a compatible interaction with U. pisi. However, in spite of this compatible interaction, high levels of rate reducing resistance were identified with significant disease severity reduction, fitting the Partial Resistance definition. Detailed histological observations showed that resistance was mainly because of haustorium formation restriction with high-level of colony early abortion, and reduction in the haustoria number per colony. This was occasionally associated with reduction on the infection hyphae intercellular growth, in a clear example of prehaustorial resistance. Differences in germination, orientated germ tube growth and appressoria differentiation were observed but were, generally, of marginal importance to explain the observed resistance levels.

Lathyrus cicera has a high potential as fodder crop in dry areas, but can in particular environments be damaged by rust. Little is known on the availability of resistance against rust fungi and the underlying mechanisms in L. cicera germplasm. The present study assessed and characterised macro and microscopically the resistance to rust fungi Uromyces pisi and U. viciae-fabae, in a collection of L. cicera accessions. A wide range of disease reaction was found in the germplasm collection against the different rust species. L. cicera accessions were highly resistant to U. viciae-fabae being hypersensitive response the most frequent reaction. On the contrary, most accessions showed a compatible interaction with U. pisi, with varying levels of partial resistance, although cases of hypersensitivity were also identified. Differences on germination, orientated germ tube growth and appressoria differentiation were observed but were in general of marginal importance to explain the resistance to U. pisi among the L. cicera accessions. Resistance was due, to a combination of pre and post-haustorial mechanisms.

Orobanche foetida is widely distributed in western Mediterranean countries infecting wild legumes. Recently it has been reported in Morocco infecting common vetch, presenting a further constraint for legume production in this area. Comparative studies between Orobanche populations attacking wild species and Orobanche populations growing on crops from the same region may help to clarify whether a host specialisation process occurred. In the present study, the genetic variability of five O. foetida populations, four infecting wild plants and one infecting cultivated vetch in Morocco was characterised using amplified fragment-length polymorphism (AFLP) markers to elucidate the existing genetic relationship between populations and to suggest a potential origin for the recently detected vetch-infecting population. Analysis of molecular variance suggested the existence of genotypic differentiation among populations. The most genetic divergent population by cluster analysis was the population collected on Ornithopus sativus. The vetch-infecting O. foetida population was closer to the three populations infecting Scorpiurus muricatus. The possibility of the presence of a reservoir of diversity is balanced against direct genetic adaptation and completely new introduction. The potential for this Orobanche species to shift host and become a threat to agriculture exists and has to be taken into account for future legume breeding for these areas.

Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer’s and Parkinson’s. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo. info:eu-repo/semantics/publishedVersion

Maps are a useful tool that permits correlation of landscapes with hotspots of parasite transmission. Here, they were used as a tool for geovisualization to evaluate variables involved in the transmission of Trypanosoma cruzi among small wild mammals in an area endemic for Chagas disease, the "Serra da Capivara" National Park (PARNA) and its surroundings in Piauí State, Northeast Brazil. The implementation of a Geographical Information System (GIS) allowed the observation that a previously noted aggregated distribution of Triatoma sordida and Triatoma brasiliensis, T. cruzi prevalence and infection pattern of small wild mammals was directly or indirectly influenced by the local relief and human action. Small mammalian species diversity was higher in mesic refugia inside the park and in its buffer zone and lower in the disturbed area by anthropic activities. Didelphis albiventris was more abundant in the areas affected by human action. Thrichomys laurentius demonstrated to be an eclectic species and a competent reservoir of T. cruzi, being infected in all study areas. Small wild mammals infected with the TCII genotype of T. cruzi were localized only in the buffer zone of PARNA while TCI infected specimens were found in both areas, inside the PARNA and its buffer zone. The impact of biodiversity loss on the transmission cycle of T. cruzi in the wild environment was discussed.

Several Lathyrus species have a considerable potential as alternative pulses in sustainable dryland farming systems mainly due to their high tolerance to drought and disease resistance. Powdery mildew is a serious disease affecting several Lathyrus species. Little is known on the availability of resistance and the underlying resistance mechanisms against powdery mildew in the Lathyrus genus. The present study assessed and characterized the resistance reaction to powdery mildew, Erysiphe pisi, in a collection of Iberian Lathyrus cicera accessions. In general, a compatible reaction with no macroscopically visible necrosis was observed but accessions with reduced disease severity despite of a high infection type have also been identified. This Partial Resistance was in some accessions only expressed in the adult plant stage. The controlling genes of the Lathyrus resistance mechanisms can be of great interest not only for the Lathyrus improvement per se but also for related legume species, like field pea.

The Portuguese maize bread (“broa”) manufactured from traditional maize landraces still plays an important economic and social role on Central and Northern rural communities of the country. However the traditional maize landraces agricultural systems are changing. Local maize landraces are in risk of disappearing because of the progressive adoption of hybrid varieties not suitable for bread production. These changes are contributing to a major loss of genetic diversity. An expedition took place in the Central region of Portugal (Beira Interior and Beira Litoral) with the purpose of collecting enduring maize landraces with technological ability for bread production and to access the possibility of establishing a participatory plant breeding and conservation program. A total of 51 different maize landraces and 175 other varieties of associated crops were collected. Maize landraces showed to maintain high diversity and potential for improvement. The production relayed on small farms with polycrop, quality oriented, sustainable systems. A participatory plant breeding and conservation program would be possible on this region with the proviso that local authorities would be involved. This program would allow a higher valuation of these maize populations, contributing to halt the current loss of these unique Portuguese maize landraces.

In this paper we review the existence of sources of resistance and the various available screening methods for resistance in grain legumes against the airborne pathogens powdery mildews, downy mildews and rusts. Available resistance against these pathogens is not abundant and is particularly in risk of erosion owing to the constant generation and introduction of new races of the pathogen. A continuous search for more resistance sources is therefore a priority in legume breeding and special emphasis should be paid to selection of resistance mechanisms that are likely to be durable and to implementation of strategies to prolong the durability of existing resistance.

Model plants are facilitating the genetic characterization and comparative mapping of a number of traditional crops. Medicago truncatula has been widely accepted as a model plant to this end as it provides the essential tools for multiple aspects of legume genetics and genomics. A large set of markers from highly conserved M. truncatula gene regions is being created and used to establish a worldwide framework for comparative genomic studies in legumes. We have investigated the potential for cross-species amplification of 209 expressed sequence tag (EST)-based and 33 bacterial artificial chromosome (BAC)-based microsatellites from M. truncatula in the three most important European legume pulses-pea, faba bean and chickpea-that might facilitate future comparative mapping. Our results revealed significant transferability of M. truncatula microsatellites to the three pulses (40% in faba bean, 36.3% in chickpea and 37.6% in pea). The percentage of M. truncatula EST-SSRs (simple sequence repeats) amplified in the three crops (39-43%) was twofold higher than that of the genomic SSRs (21-24%). Sequence analysis determined that the level of conservation in the microsatellite motif was very low, while the flanking regions were generally well conserved. The variations in the sequences were mainly due to changes in the number of repeat motifs in the microsatellite region combined with indel and base substitutions. None of the functional microsatellites showed direct polymorphism among the parental genotypes tested, consequently preventing their immediate use for mapping purposes.

The Osborne protein fractions of seeds of 17 Lupinus albus cultivars from different regions in Portugal (obtained from plants grown at the same location) were analysed. The objective of this work was to examine the variability in the seed protein fractions of such a L. albus germplasm sample in order to disclose existing genetic relationships and to obtain information useful for a breeding program. Globulins and, interestingly, the fraction extracted with NaOH (‘‘glutelins’’) were the major seed protein constituents. The several protein fractions were separated by electrophoresis (reducing SDS polyacrylamide gel electrophoresis) and the patterns examined by multivariate analysis. Bands of ‘‘glutelins’’ together with those of glycosylated polypeptides were found to have the highest discriminating capacity. Lupin populations were grouped according to their clinal geographical distribution from north (small-seeded, higher plant architecture and later flowering type) to south (large-seeded, shorter and early flowering type). It is also possible that polypeptide patterns could reflect microclimatic specificities related with altitude and temperature. In fact, one cultivar from the south but from high altitude was grouped with the north plant types adapted to colder and wetter weather, whereas two cultivars from a warmer north region were grouped with the southern types. The results show, in addition, that a general correlation exists between cultivar early flowering characteristics and higher amounts of both total seed protein and glutelins, and lower glutelin glycosylation. Since high seed protein content and early flowering are important aims of lupin breeding programs, these findings on the seed protein fractions could stimulate and direct future research in lupin improvement. # 2003 Elsevier B.V. All rights reserved.

A collection of Portuguese maize accessions representing a valuable source of genes for introduction into modern cultivars is stored at the Portuguese Plant Germplasm Bank (Banco Portugues de Germoplasma Vegetal—BPGV). To assess genetic diversity among inbreds, microsatellite analysis was carried out for 54 inbred lines representing the diversity of Portuguese dent and flint maize germplasm. Fifty American and other European elite inbreds were also analysed for comparison. Fifteen microsatellite loci distributed throughout the maize genome were chosen based on their repeat unit and base composition. A total of 80 alleles were detected with an average allele number of 5.33 per locus. Polymorphism information content (PIC) values and observed genetic distances showed the existence of large variability among inbreds. Cluster analysis indicated that almost all of the inbreds could be distinguished from each other and Portuguese inbreds were present in all clusters formed. These associations were consistent with the known pedigree records of the inbreds, confirming a mixed origin of Portuguese materials. Comparative analysis of microsatellite diversity among groups was established according to important traits for both breeding and line identification. This revealed that, although most of the genetic diversity (>95%) was attributable to differences among inbreds of different groups, the existence of phenotypic differentiation in endosperm colour, kernel type and cob colour could be suggested for grouping. These findings support the joint use of molecular and morphological traits in management of the germplasm collection. In this study, SSR markers proved to be effective to characterise and identify maize inbred lines, and demonstrate associations among them.

Although yield and total biomass produced by annual legumes remain major objectives for breeders, other issues such as environment-friendly, resource use efficiency including symbiotic performance, resilient production in the context of climate change, adaptation to sustainable cropping systems (reducing leaching, greenhouse gas emissions and pesticide residues), adaptation to diverse uses (seeds for feed, food, non-food, forage or green manure) and finally new ecological services such as pollinator protection, imply the need for definition of new ideotypes and development of innovative genotypes to enhance their commercialization. Taken as a whole, this means more complex and integrated objectives for breeders. Several illustrations will be given of breeding such complex traits for different annual legume species. Genetic diversity for root development and for the ability to establish efficient symbioses with rhizobia and mycorrhiza can contribute to better resource management (N, P, water). Shoot architectures and phenologies can contribute to yield and biotic constraint protection (parasitic weeds, diseases or insects) reducing pesticide use. Variable maturity periods and tolerance to biotic and abiotic stresses are key features for the introduction of annual legumes to low input cropping systems and for enlarging cultivated area. Adaptation to intercropping requires adapted genotypes. Improved health and nutritional value for humans are key objectives for developing new markets. Modifying product composition often requires the development of specific cultivars and sometimes the need to break negative genetic correlations with yield. A holistic approach in legume breeding is important for defining objectives with farmers, processors and consumers. The cultivar structures are likely to be more complex, combining genotypes, plant species and associated symbionts. New tools to build and evaluate them are important if legumes are to deliver their exciting potential in terms of agricultural productivity and sustainability as well as for feed and food.

There is growing awareness that fluctuations in larval flux (connectivity) depress the long-run growth of marine metapopulations, but by how much is unclear. Here, we explore how reproductive schedule and larval behavior affect how much connectivity fluctuations depress growth. We combine larval dispersal simulations from the Florida Keys with theoretical results to calculate the effect of fluctuations on bicolor damselfish (Stegastes partitus). We find that fluctuations depress growth only slightly (∼2%), but the effect would be much stronger for an organism that spawned only part of the year. Larval behavior can also matter, as vertical migration allows larvae to become entrained in eddies. Eddies synchronize connectivity fluctuations, further decreasing growth. However, here, they also divide the Keys into largely independently fluctuating regions, mitigating the effects of local synchrony. Therefore, in situations where connectivity fluctuations matter, the presence of independently fluctuating regions due to larval behavior may be important.

[Background] The Lathyrus genus includes 160 species, some of which have economic importance as food, fodder and ornamental crops (mainly L. sativus, L. cicera and L. odoratus, respectively) and are cultivated in >1·5 Mha worldwide. However, in spite of their well-recognized robustness and potential as a source of calories and protein for populations in drought-prone and marginal areas, cultivation is in decline and there is a high risk of genetic erosion. [Scope] In this review, current and past taxonomic treatments of the Lathyrus genus are assessed and its current status is examined together with future prospects for germplasm conservation, characterization and utilization. A particular emphasis is placed on the importance of diversity analysis for breeding of L. sativus and L. cicera. [Conclusions] Efforts for improvement of L. sativus and L. cicera should concentrate on the development of publicly available joint core collections, and on high-resolution genotyping. This will be critical for permitting decentralized phenotyping. Such a co-ordinated international effort should result in more efficient and faster breeding approaches, which are particularly needed for these neglected, underutilized Lathyrus species. © 2014 The Author., The authors would like to acknowledge the financial support of Fundação para a Ciência e a Tecnologia, Portugal, through grants #PEst-OE/EQB/LA0004/2011 and #PTDC/AGR-GPL/103285/2008 and Research Contract by the Ciência 2008 program (to M.C.V.P.). This research was also funded by FP7-ARIMNet-MEDILEG project and by Spanish project AGL2011-22524.

The infection process of most rust fungi start with spore germination, directional growth of the germ tube towards a stoma, differentiation of an appressorium over the stoma, and penetration into the substomatal cavity. In the South American wild barley Hordeum chilense Roem. & Schult., wide variation occurs in the degree to which several rust fungal species are able to form appressoria over the stomata. Apparently, features of the plant may hamper early stages of the infection process. Such an early defence is called avoidance. In order to find out how germ tube growth is directed towards stomata, and whether the cuticular wax layer plays a role in this orientated growth and in appressorium differentiation, several orientation and differentiation parameters of Puccinia hordei germ tubes were measured on H. chilense leaves with and without the wax layer. Orientated growth of the germ tubes started upon contact with the epidermal cell junctions. The growth of lateral branches of the germ tube over the first epidermal cell junction that it meets, may help the germ tube to grow along the transverse axis of the leaf. No evidence was found of attraction of the germ tube to stomata. Removal of the cuticular wax layer did not result in loss of germ tube orientation. This suggests that the leaf wax layer has no role in the guidance of germ tubes. On high avoidance accessions, removal of the wax layer allowed appressoria to develop over stomata that would otherwise be overgrown. No effect of the cell widths in stomatal complexes was found on the chance that stomata were overgrown. This suggests that the overgrowth of stomata on H. chilense leaves by P. hordei germ tubes is mainly caused by the wax covering of the stomatal apparatus.

Seven F2 families of faba bean descendent from plants trisomic for chromosomes 3, 4, 5 and 6 were analyzed for isozyme markers and two of these were also studied for morphological and RAPD markers and seed-protein genes. Linkage analysis revealed 14 linkage groups, 8 of which were unambiguously assigned to specific chromosomes. Several QTLs for seed weight were identified, the most important of which, located on chromosome 6, explained approximately 30% of the total phenotypic variation. Comparison of results from Vicia faba with the maps of the related species Pisum sativum L. and Cicer arietinum L. revealed one possible new case of linkage conservation. A composite linkage analysis based on 42 markers analyzed in this and previous studies, where line Vf 6 was also used as the female parental, allowed the new assignment of previously independent linkage groups and/or markers to specific chromosomes. Thus, the number of linkage groups was reduced to 13, each comprising an increased number of markers. No contradictory results were detected, indicating the suitability of the statistical procedure and methodology used so far in the development of the map of this species.

Lathyrus sativus has a considerable potential for dry land-farming systems but can be severely damaged by powdery mildew infection. Little is known about the availability of resistance against powdery mildew and the underlying mechanisms in the Lathyrus genus. A range of resistance reactions was identified in a collection of Iberian-cultivated L. sativus germplasm. In most cases a compatible reaction to powdery mildew with no macroscopically visible necrosis was observed. Nevertheless, accessions with reduced disease severity despite being of a high infection type have been identified. The genes responsible for this partial resistance will be potentially useful for the development of durable resistant cultivars of Lathyrus spp., and may also be of value for the improvement of other related cultivated leguminous plants.

Question: How reliable is the process of delimiting plant species by morphotyping sterile specimens from a highly diverse Amazonian forest plot? Location: Biological Dynamics of Forest Fragments Project (BDFFP), Central Amazon, Manaus, Brazil. Methods: A taxonomic exercise was conducted during a Center for Tropical Forest Science (CTFS) Taxonomy Workshop held in Manaus in April 2011, using specimens collected in a 25-ha forest plot.The plant species from this plot had been previously delimited by morphotyping of ca. 80 000 sterile specimens, a process that resulted in the recognition of 115 cases (accounting for 38% of all trees) in which species delimitation was problematic. For the workshop, we selected a subsample of specimens for eight of these difficult cases (taxonomic groups/complexes) and asked 14 participants with different levels of botanical training to independently sort these specimens into morphospecies. We then compared the classifications made by all participants and explored correlations between botanical training and plant classification. Results: The classification of specimens into morphospecies was highly variable among participants, except for one taxonomic group/complex, for which the median pair-wise similarity was 95%. For the other seven taxonomic groups/complexes, median pair-wise similarity values ranged from 52% to 67%. Training did not increase the similarity in the definition of morphospecies except for two taxonomic groups/complexes, for which there was higher congruence between the classifications made by participants with a high level of botanical training than in comparisons that included less-experienced participants. The total number of morphospecies defined by participants was highly variable for all taxonomic groups/complexes, with the total number varying from 12 to 46 (a 383% difference). Conclusions: Local plant species delimitation by morphotyping sterile specimens is prone to large uncertainties, and botanical training may not reduce them. We argue that uncertainty in species delimitation should be explicitly considered in plant biodiversity inventories as diversity estimates may be strongly affected by such uncertainties. We recommend that species delimitation and identification be treated as separate processes and that difficulties be explicitly recorded, so as to permit error estimates and the refinement of taxonomic data.

Alginate and Aloe vera are natural materials widely investigated and used in the biomedical field. In this research work, thin hydrogel films composed by alginate and Aloe vera gel in different proportions (95:5, 85:15 and 75:25, v/v) were prepared and characterized. The films were evaluated regarding the light transmission behavior, contact angle measurements, and chemical, thermal and mechanical properties. These thin hydrogel films, prepared by crosslinking reaction using 5% calcium chloride solution, were also investigated relatively to their water solubility and swelling behavior. Results showed that Aloe vera improved the transparency of the films, as well their thermal stability. The developed films present adequate mechanical properties for skin applications, while the solubility studies demonstrated the insolubility of the films after 24 h of immersion in distilled water. The water absorption and swelling behavior of these films were greatly improved by the increase in Aloe vera proportion. info:eu-repo/semantics/publishedVersion

Transthyretin (TTR) is a homotetrameric protein implicated in several amyloid diseases. The mechanism by which TTR is converted into elongated fibrillar assemblies has been extensively investigated, and numerous studies showed that dissociation of the native tetrameric structure into partially unfolded monomeric species precedes amyloid formation. The small differences observed in the crystal structures of different TTR variants, as well as the thermodynamics and kinetics of tetramer dissociation, do not seem to completely justify the amyloidogenic potential of different TTR variants. With this in mind, we have studied the refolding kinetics of WT-TTR and its most common amyloidogenic variant V30M-TTR, monitoring changes in intrinsic tryptophan fluorescence at different urea and protein concentrations. Our results demonstrate that thein vitrorefolding mechanisms of WT- and V30M-TTR are similar, involving a dimeric intermediate. However, there are large differences in the refolding rate constants for the two variants, specially close to physiological conditions. Interestingly, tetramer formation occurs at a much slower rate in the amyloidogenic variant V30M-TTR than in WT-TTR, which in thein vivosetting may promote the accumulation of monomeric species in the extracellular environment, resulting in higher susceptibility for aggregation and amyloid formation instead of spontaneous refolding.

Newton, A. C. et al., Modern agriculture and conventional breeding and the liberal use of high inputs has resulted in the loss of genetic diversity and the stagnation of yields in cereals in less favourable areas. Increasingly landraces are being replaced by modern cultivars which are less resilient to pests, diseases and abiotic stresses and thereby losing a valuable source of germplasm for meeting the future needs of sustainable agriculture in the context of climate change. Where landraces persist there is concern that their potential is not fully realised. Much effort has gone into collecting, organising, studying and analysing landraces recently and we review the current status and potential for their improved deployment and exploitation, and incorporation of their positive qualities into new cultivars or populations for more sustainable agricultural production. In particular their potential as sources of novel disease and abiotic stress resistance genes or combination of genes if deployed appropriately, of phytonutrients accompanied with optimal micronutrient concentrations which can help alleviate aging-related and chronic diseases, and of nutrient use efficiency traits.We discuss the place of landraces in the origin of modern cereal crops and breeding of elite cereal cultivars, the importance of on-farm and ex situ diversity conservation; how modern genotyping approaches can help both conservation and exploitation; the importance of different phenotyping approaches; and whether legal issues associated with landrace marketing and utilisation need addressing. In this review of the current status and prospects for landraces of cereals in the context of sustainable agriculture, the major points are the following: (1) Landraces have very rich and complex ancestry representing variation in response to many diverse stresses and are vast resources for the development of future crops deriving many sustainable traits from their heritage. (2) There are many germplasm collections of landraces of the major cereals worldwide exhibiting much variation in valuable morphological, agronomic and biochemical traits. The germplasm has been characterised to variable degrees and in many different ways including molecular markers which can assist selection. (3) Much of this germplasm is being maintained both in long-term storage and on farm where it continues to evolve, both of which have their merits and problems. There is much concern about loss of variation, identification, description and accessibility of accessions despite international strategies for addressing these issues. (4) Developments in genotyping technologies are making the variation available in landraces ever more accessible. However, high quality, extensive and detailed, relevant and appropriate phenotyping needs to be associated with the genotyping to enable it to be exploited successfully. We also need to understand the complexity of the genetics of these desirable traits in order to develop new germplasm. (5) Nutrient use efficiency is a very important criterion for sustainability., Landrace material offers a potential source for crop improvement although these traits are highly interactive with their environment, particularly developmental stage, soil conditions and other organisms affecting roots and their environment. (6) Landraces are also a potential source of traits for improved nutrition of cereal crops, particularly antioxidants, phenolics in general, carotenoids and tocol in particular. They also have the potential to improve mineral content, particularly iron and zinc, if these traits can be successfully transferred to improved varieties. (7) Landraces have been shown to be valuable sources of resistance to pathogens and there is more to be gained from such sources. There is also potential, largely unrealised, for disease tolerance and resistance or tolerance of pest and various abiotic stresses too including to toxic environments. (8) Single gene traits are generally easily transferred from landrace germplasm to modern cultivars, but most of the desirable traits characteristic of landraces are complex and difficult to express in different genetic backgrounds. Maintaining these characteristics in heterogeneous landraces is also problematic. Breeding, selection and deployment methods appropriate to these objectives should be used rather than those used for high input intensive agriculture plant breeding. (9) Participatory plant breeding and variety selection has proven more successful than the approach used in high input breeding programmes for landrace improvement in stress-prone environments where sustainable approaches are a high priority. Despite being more complex to carry out, it not only delivers improved germplasm, but also aids uptake and communication between farmers, researchers and advisors for the benefit of all. (10) Previous seed trade legislation was designed primarily to protect trade and return royalty income to modern plant breeders with expensive programmes to fund. As the desirability of using landraces becomes more apparent to achieve greater sustainability, legislation changes are being made to facilitate this trade too. However, more changes are needed to promote the exploitation of diversity in landraces and encourage their use., We thank the European Union for funding the COST Action 860 “Sustainable variety development for low-input and organic agriculture” (2004–2008) through which this review was initiated.

The extent and pattern of genetic differentiation between Phelipanche ramosa populations colonising tobacco in different European regions were investigated by amplified fragment length polymorphism (AFLP) analysis, in order to determine levels of variation for tobacco resistance breeding and management programmes. Four different AFLP primer pairs amplified a total of 1050 clear and reproducible bands, of which 962 (91.62%) were polymorphic among the 35 individuals taken from four P. ramosa populations collected in Spain, Italy, Bulgaria and Germany. Cluster analysis based on the AFLP data categorised the plants into distinct groups, in line with their geographical origin, denoting clear genetic differentiation among the four populations. This differentiation was supported by both high bootstrap values and significant results of the analysis of molecular variance. The most divergent population was the one from Bulgaria. The majority of the genetic diversity was attributable to differences among populations (77.80%), as expected from the predominant autogamous behaviour of this species. Populations differed significantly in within-population diversity, as measured by Shannon's information index. The German population presented the lowest genetic diversity and the Italian population harboured the highest level of within-population genetic diversity. There are significant differences in genetic diversity level among the studied P. ramosa populations and clear population-specific genetic diversity structures. These need to be taken into account, together with the potential differences in parasite aggressiveness, when planning breeding and management strategies for P. ramosa control in tobacco cultivation.

The Patos Lagoon estuary is an important environment for the life cycle of many species, including the pink shrimp Farfantepenaeus paulensis. This area acts as a nursery ground for the shrimp larvae, which are spawned in a coastal area and transported into the lagoon during spring and early summer (September to December). Harvesting of shrimp occurs from January to May, and yields have varied from around 1,000 to 8,000 tons year−1. This study is based on analysis of river discharge, pink shrimp catches, and wind velocity time series from 1964 to 2004. Negative correlation between pink shrimp catches and river runoff reflects the influence of discharge on the lagoon circulation and, consequently, on the intrusion of salt water and larvae. When river discharge is below average, landward currents forced by SW winds can enhance larval transport into the estuarine area, leading to an increase in pink shrimp captures. Above average river input would force a seaward flow that works as a barrier to ingress of larvae. This is unusual when compared to many other estuarine systems, and the main factor that accounts for this behavior is the morphology (choking) of Patos Lagoon. Interannual variability related to El Nino/Southern Oscillation events also influence pink shrimp production in this area. Low/high shrimp catches are related to El Nino (flood)/La Nina (drought) events. Wind can also impact production through its effect on the southward displacement of larvae from the spawning area. Long-term trends indicate an increase in river discharge around 20 m3 s−1year−1 and a decrease in shrimp catches on the order of 57 tons year−1.

Modern agriculture and conventional breeding and the liberal use of high inputs has resulted in the loss of genetic diversity and the stagnation of yields in cereals in less favourable areas. Increasingly landraces are being replaced by modern cultivars which are less resilient to pests, diseases and abiotic stresses and thereby losing a valuable source of germplasm for meeting the future needs of sustainable agriculture in the context of climate change. Where landraces persist there is concern that their potential is not fully realised. Much effort has gone into collecting, organising, studying and analysing landraces recently and we review the current status and potential for their improved deployment and exploitation, and incorporation of their positive qualities into new cultivars or populations for more sustainable agricultural production. In particular their potential as sources of novel disease and abiotic stress resistance genes or combination of genes if deployed appropriately, of phytonutrients accompanied with optimal micronutrient concentrations which can help alleviate aging-related and chronic diseases, and of nutrient use efficiency traits. We discuss the place of landraces in the origin of modern cereal crops and breeding of elite cereal cultivars, the importance of on-farm and ex situ diversity conservation; how modern genotyping approaches can help both conservation and exploitation; the importance of different phenotyping approaches; and whether legal issues associated with landrace marketing and utilisation need addressing. In this review of the current status and prospects for landraces of cereals in the context of sustainable agriculture, the major points are the following: (1) Landraces have very rich and complex ancestry representing variation in response to many diverse stresses and are vast resources for the development of future crops deriving many sustainable traits from their heritage. (2) There are many germplasm collections of landraces of the major cereals worldwide exhibiting much variation in valuable morphological, agronomic and biochemical traits. The germplasm has been characterised to variable degrees and in many different ways including molecular markers which can assist selection. (3) Much of this germplasm is being maintained both in long-term storage and on farm where it continues to evolve, both of which have their merits and problems. There is much concern about loss of variation, identification, description and accessibility of accessions despite international strategies for addressing these issues. (4) Developments in genotyping technologies are making the variation available in landraces ever more accessible. However, high quality, extensive and detailed, relevant and appropriate phenotyping needs to be associated with the genotyping to enable it to be exploited successfully. We also need to understand the complexity of the genetics of these desirable traits in order to develop new germplasm. (5) Nutrient use efficiency is a very important criterion for sustainability. Landrace material offers a potential source for crop improvement although these traits are highly interactive with their environment, particularly developmental stage, soil conditions and other organisms affecting roots and their environment. (6) Landraces are also a potential source of traits for improved nutrition of cereal crops, particularly antioxidants, phenolics in general, carotenoids and tocol in particular. They also have the potential to improve mineral content, particularly iron and zinc, if these traits can be successfully transferred to improved varieties. (7) Landraces have been shown to be valuable sources of resistance to pathogens and there is more to be gained from such sources. There is also potential, largely unrealised, for disease tolerance and resistance or tolerance of pest and various abiotic stresses too including to toxic environments. (8) Single gene traits are generally easily transferred from landrace germplasm to modern cultivars, but most of the desirable traits characteristic of landraces are complex and difficult to express in different genetic backgrounds. Maintaining these characteristics in heterogeneous landraces is also problematic. Breeding, selection and deployment methods appropriate to these objectives should be used rather than those used for high input intensive agriculture plant breeding. (9) Participatory plant breeding and variety selection has proven more successful than the approach used in high input breeding programmes for landrace improvement in stress-prone environments where sustainable approaches are a high priority. Despite being more complex to carry out, it not only delivers improved germplasm, but also aids uptake and communication between farmers, researchers and advisors for the benefit of all. (10) Previous seed trade legislation was designed primarily to protect trade and return royalty income to modern plant breeders with expensive programmes to fund. As the desirability of using landraces becomes more apparent to achieve greater sustainability, legislation changes are being made to facilitate this trade too. However, more changes are needed to promote the exploitation of diversity in landraces and encourage their use. © 2011 Springer Science+Business Media B.V.

Germline mutations that inactivate BRCA1 are responsible for breast and ovarian cancer susceptibility. One possible outcome of genetic testing for BRCA1 is the finding of a genetic variant of uncertain significance for which there is no information regarding its cancer association. This outcome leads to problems in risk assessment, counseling and preventive care. The purpose of the present study was to functionally evaluate seven unclassified variants of BRCA1 including a genomic deletion that leads to the in-frame loss of exons 16/17 (Delta exons 16/17) in the mRNA, an insertion that leads to a frameshift and an extended carboxy-terminus (5673insC), and five missense variants (K1487R, S1613C, M1652I, Q1826H and V1833M). We analyzed the variants using a functional assay based on the transcription activation property of BRCA1 combined with supervised learning computational models. Functional analysis indicated that variants S1613C, Q1826H, and M1652I are likely to be neutral, whereas variants V1833M, Delta exons 16/17, and 5673insC are likely to represent deleterious variants. In agreement with the functional analysis, the results of the computational analysis also indicated that the latter three variants are likely to be deleterious. Taken together, a combined approach of functional and bioinformatics analysis, plus structural modeling, can be utilized to obtain valuable information pertaining to the effect of a rare variant on the structure and function of BRCA1. Such information can, in turn, aid in the classification of BRCA1 variants for which there is a lack of genetic information needed to provide reliable risk assessment.

SUMMARYExpansion of human activities frequently results in habitat fragmentation, a phenomenon that has been widely recognized in the last decades as one of the major threats to world's biodiversity. The transformation of a continuous forest into a fragmented area results in a hyper-dynamic landscape with unpredictable consequences to overall ecosystem health. The effect of the fragmentation process on Trypanosoma cruzi infection among small wild mammals was studied in an Atlantic Rain Forest landscape. Comparing continous forest to fragmented habitat, marsupials were less abundant than rodents in the continuous landscape. An overall decrease in small wild mammal richness was observed in the smaller fragments. An anti-T. cruzi seroprevalence of 18% (82/440) was deteced by immunofluorescence assay. Moreover, this seroprevalence was higher in the fragmented habitat than in the continuous forest. According to the collected data, 3 main factors seem to modulate infection by T. cruzi in small wild mammals: (i) habitat fragmentation; (ii) biodiversity loss; (iii) increase of marsupial abundance in mammal communities. Furthermore, an extremely mild controlled infection by T. cruzi was detected since no patent parasitaemia could be detected in fresh blood samples, and no parasites were isolated by haemoculture.

Several Lathyrus species and in particular Lathyrus sativus (grass pea) have great agronomic potential as grain and forage legume, especially in drought conditions. Grass pea is rightly considered as one of the most promising sources of calories and protein for the vast and expanding populations of drought-prone and marginal areas of Asia and Africa. It is virtually the only species that can yield high protein food and feed under these conditions. It is superior in yield, protein value, nitrogen fixation, and drought, flood and salinity tolerance than other legume crops. Lathyrus species have a considerable potential in crop rotation, improving soil physical conditions; reducing the amount of disease and weed populations, with the overall reduction of production costs. Grass pea was already in use in Neolithic times, and presently is considered as a model crop for sustainable agriculture. As a result of the little breeding effort invested in it compared to other legumes, grass pea cultivation has shown a regressive pattern in many areas in recent decades. This is due to variable yield caused by sensitivity to diseases and stress factors and above all, to the presence of the neurotoxin β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), increasing the danger of genetic erosion. However, both L. sativus and L. cicera are gaining interest as grain legume crops in Mediterranean-type environments and production is increasing in Ethiopia, China, Australia and several European countries. This paper reviews research work on Lathyrus breeding focusing mainly on biotic and abiotic resistance improvement, and lists current developments in biotechnologies to identify challenges for Lathyrus improvement in the future.

Introduction: Elastomeric ligatures are observed to reduce chair side time; however, they are also seen to have greater bacterial adhesion. Polymeric coating utilizing the Metafasix Technology and the OrthoShield Technology have been introduced in the Super Slick™FNx01 and Safe-T-Ties™FNx08 by TP Orthodontics, Ortho Organizers, respectively, to reduce bacterial adhesion. While each of the elastomers has been individually evaluated, no study compares the two elastomers manufactured by differing technologies together; hence the need for this study was felt. This in vivo study compared the Super Slick and Safe-T-Ties with their unmodified counterparts for bacterial adhesion. Materials and Methods: Thirty patients undergoing orthodontic treatment, between 12 and 25 years age group were selected and the modified, and the unmodified elastomers were randomly placed quadrant wise, on all the premolar brackets. After a period of 4 weeks, the elastomeric rings were removed and transported for culture on Mitis-Salivarius, Rogosa SL agar for Streptococcus mutans and Lactobacilli, respectively. The colonies were digitally counted (HiMedia) after 48 h of incubation at 37°C. Results: There was a significant difference in the S. mutans and Lactobacilli counts in both surface modified and unmodified elastomeric modules (P < 0.01). Unmodified elastomeric modules Mini Stix™FNx01, Hand-EE-Lasts™FNx08 was associated with higher mean values of colony-forming units/millimeter than the surface modified Super Slick™FNx01 and Safe-T-Ties™FNx08 ligatures. When compared pair-wise, the surface modified elastomers showed less bacterial accumulations than the unmodified counterparts for both S. mutans and Lactobacillus, and the differences were statistically significant. Conclusion: Technological modifications of the elastomers using the Metafasix or OrthoShield Technology, is a definite improvement over the regular elastomers with regard to adhesion of S. mutans and Lactobacilli.