Sulfamethoxazole biodegradation and impacts on soil microbial communities in a Bolivian arid high altitude catchment.

The processes controlling antibiotics fate in ecosystems are poorly understood, yet their presence can inhibit bacterial growth and induce the development of bacterial resistance. Sulfamethoxazole (SMX) is one of the most frequently detected sulfonamides in natural environments due to its low metabolism and molecular properties. This work presents pioneering results on SMX biodegradation and impact in high altitude soils (Bolivian Altiplano), allowing a better understanding of the persistence, spread and impact of this antibiotic at the global watershed scale. Our results showed significant dissipation of SMX in relation to its adsorption, hydrolysis and biotransformation. However, biodegradation appears to be lower in these mountain soils than in lowland soils as widely described in the literature. The half-life of SMX ranges from 12 to 346 days in non-sterile soils. In one soil, no biotic degradation was observed, indicating a likely high persistence. Biodegradation was related to OC content and to proximity to urban activities. Regarding the study of the impacts of SMX, the DGGE results were less sensitive than the sequencing. In general, SMX strongly changes the structure and composition of the studied soils at high altitudes, which is comparable to the observations of other authors in lowland soils. The phylum Actinobacter showed high sensitivity to SMX. In contrast, the abundance of ɣ-proteobacteria remained almost unchanged. Soil contamination with SMX did not lead to the development of the studied resistance genes (sul1 and sul2) in soils where they were absent at the beginning of the experiment. Thus, the presence of SMX resistance genes seems to be related to irrigation with wastewater carrying the studied resistance genes.

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds.

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states.

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

Quantificação do DNA e genotipagem de biópsias de embriões bovinos Gir e Girolando produzidos in vitro / DNA quantification and genotyping of biopsies obtained from Gyr and Girolando in vitro produced bovine embryos

A biópsia embrionária associada à genotipagem permite a obtenção de informações genômicas antes mesmo da transferência dos embriões. Neste estudo, foram avaliadas amostras biopsiadas de blastocistos bovinos transferidos para receptoras (n=47), sob a hipótese de que a raça (Gir ou Girolando), o estádio embrionário (blastocisto ou blastocisto expandido) e a competência para estabelecimento de prenhez (positiva ou negativa) afetariam a quantidade e a qualidade do DNA da amostra obtida. O DNA foi extraído, amplificado, quantificado por eletroferograma e genotipado. O parâmetro call rate (CR) foi adotado para mensurar a qualidade da genotipagem. Obteve-se concentração de DNA de 86,07±171,66ng/µL e CR 0,73±0,17. O CR não variou em função da quantidade de DNA nas amostras. As variáveis raça e estádio embrionário não influenciaram a concentração de DNA, nem o CR. Houve efeito da prenhez sobre o CR (P=0,0187), mas, como houve maior CR nas amostras provenientes do grupo prenhez negativa, não foi possível associar esse parâmetro à qualidade embrionária. Concluiu-se que a raça e a qualidade embrionária não afetam os parâmetros aqui estudados em amostras embrionárias, ou seja, embriões com maiores chances de implantação não refletem alta qualidade nas amostras de biópsia genotipadas.(AU)

Embryo biopsy associated with genotyping allows genomic information before embryo transfer. In this study, blastocyst biopsy samples from embryos transferred to recipients (n= 47) were evaluated, under the hypothesis that breed (Gyr or Girolando), embryonic stage (blastocyst or expanded blastocyst) and competence to establish pregnancy (positive or negative) would affect the quantity and DNA quality of samples. DNA was extracted, amplified, quantified by electropherogram and genotyped. The parameter call rate (CR) was used to measure the quality of genotyping. DNA concentration of 86.07±171.66ng/µl, and CR 0.73±0.17 was obtained. CR did not vary according to the amount of DNA in the samples. The variables breed and embryonic stage had no influence on DNA concentration or CR. There was pregnancy effect on the CR (P= 0.0187), but since there was a higher CR in the samples from the negative pregnancy group, it was not possible to associate this parameter with the embryonic quality. We conclude that the breed and embryo quality do not affect the evaluated parameters in embryonic samples. Embryos with higher chances of implantation do not reflect high quality in embryo biopsy genotyped samples.(AU)

Growth, blood, carcass and meat quality traits from local pig breeds and their crosses.

Contrary to intensive pig production, local pig breeds and their production systems are able to respond to the high criteria and expectations of modern society in regard to some environmental aspects, animal welfare, food quality and healthiness. This study proposes the recovery, study and use of a cross between two local breeds, contributing to animal biodiversity conservation and to the income of local pig producers. This work studied the growth performance and blood, carcass and meat quality traits of Alentejano (AL), Bísaro (BI) and Ribatejano (RI) (AL × BI, BI × AL) castrated male pigs. Raised outdoors, pigs were fed commercial diets ad libitum and killed at ~65 kg (trial 1, n = 10 from each genotype) and ~150 kg BW (trial 2, n = 9 from each genotype). In trial 1, AL and AL × BI attained slaughter weight later than BI and BI × AL pigs, with AL presenting lower average daily gains than the other genotypes (P < 0.001). Alentejano and RI pigs presented higher (P < 0.01) levels of plasma total protein than BI. Overall, carcass traits were affected by genotype, with length (P < 0.01), yield (P = 0.07) and lean cut proportions (P < 0.01) lower in AL than BI, and intermediate values for crossed pigs. Conversely, AL pigs presented higher fat cut proportion (P < 0.01), average backfat thickness (P < 0.001) and 'zwei punkte' fat depth (P < 0.01) than BI and RI pigs. Alentejano pigs also presented higher Longissimus lumborum (LL) intramuscular fat (P < 0.05), myoglobin content and ultimate pH (P < 0.01), but lower total collagen (P < 0.05), drip (P < 0.001) and cooking losses (P < 0.01), and shear force (P < 0.001) than all other genotypes. Finally, LL showed a more intense red colour in AL than in BI pigs. In trial 2, AL pigs confirmed to be a slow-growing obese breed with lower bone and lean cut proportions than BI, and higher LL intramuscular fat, richer colour, lower water loss and higher tenderness. In both trials, RI pigs grew faster, with higher lean and lower fat cut proportions and backfat thickness, and with overall LL characteristics comparable to those observed in AL pigs. This work demonstrates some clear differences between AL and BI breeds while showing that their crosses present intermediate characteristics in most studied traits. These data on RI pigs can be useful to breeders' associations and farmers in order to consider the use of these crosses as an option or complement to pure line breeding.

Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip.

Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

Assessment of the Sulfamethoxazole mobility in natural soils and of the risk of contamination of water resources at the catchment scale.

Sulfamethoxazole (SMX) is one of the antibiotics most commonly detected in aquatic and terrestrial environments and is still widely used, especially in low income countries. SMX is assumed to be highly mobile in soils due to its intrinsic molecular properties. Ten soils with contrasting properties and representative of the catchment soil types and land uses were collected throughout the watershed, which undergoes very rapid urban development. SMX displacement experiments were carried out in repacked columns of the 10 soils to explore SMX reactive transfer (mobility and reactivity) in order to assess the contamination risk of water resources in the context of the Bolivian Altiplano. Relevant sorption processes were identified by modelling (HYDRUS-1D) considering different sorption concepts. SMX mobility was best simulated when considering irreversible sorption as well as instantaneous and rate-limited reversible sorption, depending on the soil type. SMX mobility appeared lower in soils located upstream of the watershed (organic and acidic soils - Regosol) in relation with a higher adsorption capacity compared to the soils located downstream (lower organic carbon content - Cambisol). By combining soil column experiments and soil profiles description, this study suggests that SMX can be classified as a moderately to highly mobile compound in the studied watershed, depending principally on soil properties such as pH and OC. Potential risks of surface and groundwater pollution by SMX were thus identified in the lower part of the studied catchment, threatening Lake Titicaca water quality.

Suplementação proteica de vacas leiteiras mantidas em pastagem de Tifton 85 durante o período de seca / Protein supplementation of dairy cows grazing Tifton 85 during the dry season

Concentrados com alta proteína bruta e minerais e com menor concentração de energia poderiam ser utilizados em menores quantidades no balanceamento de dietas com volumosos tropicais. Assim, objetivou-se avaliar o consumo de matéria seca, a resposta produtiva e econômica de vacas da raça Girolando mantidas em pastagem de Tifton 85 durante o período de seca, as quais receberam diferentes concentrações de suplementação proteica. Foram utilizadas 12 vacas da raça Girolando em lactação, com produção de leite média inicial de 18,00±1,615kg/dia. Os animais foram distribuídos em três quadrados latinos (4x4), constituídos de quatro tratamentos e quatro períodos experimentais, com duração de 15 dias cada. Os tratamentos consistiram de uma dieta controle, apenas sal mineral e três níveis de suplementação proteica com 40; 50 e 60% de proteína bruta (PB) sendo fornecidas nas quantidades de 2,5kg/animal/dia. Observou-se que os fornecimentos de suplementos proteicos proporcionaram um efeito substitutivo da forragem em relação à suplementação mineral. O uso de suplementação concentrada com teor de 40% de proteína bruta foi mais eficiente em termos produtivos, econômicos e de produção de proteína bruta no leite.(AU)

Concentrates with high crude protein and minerals and lower energy concentration could be used in smaller quantities in balancing diets with tropical bulk. The objective of this study was to evaluate the dry matter intake, the productive and economical response of Girolando cows kept in Tifton 85 pasture during dry season receiving different concentrations of protein supplementation. Twelve lactating Girolando cows with initial mean milk yield of 18.00±1.615kg/day were used. The animals were distributed in three Latin squares (4x4), consisting of four treatments and four experimental periods, each lasting 15 days. The treatments were composed of control diet with only mineral salt, and three levels of protein supplementation with 40, 50, and 60% crude protein (CP) being supplied in the amounts of 2.5kg/animal/day. It was found that the protein supplement supplies provided a substitutive effect of forage relative to mineral supplementation. The use of concentrated supplementation with 40% crude protein content was more efficient in terms of production, production of crude protein in milk and economically.(AU)

Internal quality control indicators in cervical cytopathology of a university laboratory.

INTRODUCTION: To evaluate the internal quality control indicators and quality management programme in a university cytopathology laboratory. METHODS: All results of conventional cervical smears tests (taken from the SISCAN, the Brazilian cervical cancer screening system) of women aged ≥15 years at the time of Papanicolaou smear specimen collection during January 2007-December 2014 were included. The final results of the cytopathology were classified in accordance with the Bethesda System. The variables included in the database were the woman's name, date of birth, and age at the time of sampling (15-30, 31-40 and older than 40 years). RESULTS: In this period, 50 286 cytopathology examinations were carried out. Of these, 44 386 (91.34%) were negative for malignancy or unsatisfactory and 4209 (8.66%) presented epithelial abnormalities. The percentage of the tests consistent with atypical squamous cells (ASC) between satisfactory examinations was 4.12%; the percentage of tests compatible with ASC among abnormal examinations was 47.87%; the ASC/squamous intraepithelial lesion) ratio was 0.97 and the percentage of high-grade squamous intraepithelial lesion among satisfactory tests was 2.21%, and the 5-year retrospective review identified 4.97% of false-negative results. CONCLUSION: All rates obtained were consistent over the years and within the recommended values by Federal Regulation of Brazil. This demonstrates the efficacy of our established internal quality monitoring and continuing education, reflecting the commitment of the team involved in the release of smear reports.

Influence of outdoor rearing and oleic acid supplementation on lipid characteristics of muscle and adipose tissues from obese Alentejano pigs.

Data evaluating the effect of oleic-acid-enriched diets and outdoor rearing (with access to pasture) on the quality of Alentejano (AL) pork and fat are limited. The aim of this work was to study the effects of feeding low (LO) or high oleic acid (HO) diets to AL pigs reared in individual pens (IND) or outdoors (OUT) with access to pasture. Biceps femoris and dorsal subcutaneous fat (DSF) samples were collected to analyse chemical composition and lipids fatty acid (FA) profile. The expression of seven genes involved in lipogenesis, lipolysis and FA transport, as well as two transcription factors were also evaluated in the muscle. B. femoris and DSF presented lower lipid content in OUT-reared than in IND-reared pigs. Two genes involved in lipogenesis, ACACA and FASN, were under-expressed in B. femoris from OUT-reared pigs, while two involved in lipolysis, LPL and HSL were over-expressed. HO diet also significantly reduced FASN expression. Both rearing system and diet affected the FA profile of tissues, particularly DSF. Overall, OUT-reared pigs presented lower n6 to n3 FA ratios in all tissues, and lower monounsaturated (MUFA) and higher polyunsaturated fatty acids (PUFA) content in DSF. When compared to LO-fed ones, HO-fed pigs presented higher oleic acid proportions in all tissues, and lower SFA, higher MUFA and PUFA levels, as well as lower saturation, atherogenic and thrombogenic indexes in DSF. This study shows that rearing system and oleic acid supplementation have complementary effects and influence the nutritional quality of pork and DSF.

The unexpected role of bioaerosols in the Oxidative Potential of PM.

Bioaerosols represent up to 15-25% of PM by mass, but there is currently no assessment of their impact on Oxidative Potential (OP), or capacity of particulate matter (PM) to produce damaging oxidative reactions in the human lungs. Here, the OP of selected bioaerosols (bacteria cells vs fungal spores) was assessed through the cell-free DTT assay. Results show that bioaerosols induce Reactive Oxygen Species (ROS) production, varying along the microorganism type, species, and concentration. Fungal spores show up to 10 times more ROS generation than bacterial cells. At the highest concentrations, fungal spores present as much oxidative reactivity as the most redox-active airborne chemicals (Copper, Naphtoquinone). Moreover, bioaerosols substantially influence OP of ambient PM and that of its chemical constituents: in presence of A. fumigatus spores, the OP of Cu/NQ is increased by a factor of 2 to 5, whereas, 104 and 105 S. epidermidis bacterial cells.mL-1 halves the OP of Cu/NQ. Finally, viable and gamma-rays-killed model bioaerosols present similar oxidative reactivity, suggesting a metabolism-independent cellular mechanism. These results reveal the importance of bioaerosols for PM reactivity. PM toxicity can be modified due to bioaerosols contribution or by their ability to modulate the OP of toxic chemicals present in PM.

Very late presentation of a disorder of sex development.

Disorders of sex development generally present in the neonatal period with ambiguity of external genitalia. We report a very old male patient presenting at 75 years because of panhypopituitarism and a large nonsecreting pituitary macroadenoma secondary to long-standing primary hypogonadism due to 46,XX sex reversal disorder now first diagnosed. Sex development disorders may go unrecognised for the entire life span, despite infertility and long-standing primary gonadic failure may lead to uncommon complications.

Antibiotic pollution in the Katari subcatchment of the Titicaca Lake: Major transformation products and occurrence of resistance genes.

An increasing number of studies pointed out the ubiquitous presence of medical residues in surface and ground water as well as in soil compartments. Not only antibiotics can be found in the environment but also their transformation products about which little information is generally available. The development of bacterial resistance to antibiotics is particularly worrying as it can lead to sanitary and health problems. Studies about the dissemination of antibiotics and associated resistances in the Bolivian Altiplano are scarce. We provide baseline information on the occurrence of Sulfamethoxazole (SMX) and Trimethoprim (TMP) antibiotics as well as on the most common human SMX transformation products (TP) and on the occurrence of sulfonamide resistance genes. The studied water and soil compartments presented high levels of antibiotic pollution. This situation was shown to be mainly linked with uncontrolled discharges of treated and untreated wastewaters, resulting on the presence of antibiotics in the Titicaca Lake. SMX TPs were detected in surface waters and on soil sampled next to the wastewater treatment plant (WWTP). SMX resistance genes sulI and sulII were widely detected in the basin hydrological network, even in areas unpolluted with antibiotics. Mechanisms of co-selection of antibiotic- and metal- resistance may be involved in the prevalence of ARG's in pristine areas with no anthropogenic activity and free of antibiotic pollution.

Proteomic analysis of seminal plasma and sperm cells and their associations with semen freezability in Guzerat bulls.

The objective of the present study was to describe the relationship of seminal plasma and total sperm cell proteins with the semen freezability parameters of Guzerat bulls. Thirteen bulls were subjected to breeding soundness evaluation. Semen samples were collected, cryopreserved, and then post-thawing sperm kinetics were assessed, where high ( = 7) and low ( = 6) freezability groups were defined. Seminal plasma and total sperm proteins from the 2 groups were separated by 2-dimensional SDS-PAGE, and spots were identified by mass spectrometry. Semen parameters post-cryopreservation were as follows in the high and low freezability groups, respectively: mean total motility, 52.4 ± 20.5 and 13.7 ± 3.9; percentage of normal sperm, 89.0 ± 2.6 and 64.7 ± 14.0; and reactivity of hypo-osmotic swelling test, 38.9 ± 4.7 and 13.6 ± 3.7. Three seminal plasma proteins (osteopontin-K, DNase γ precursor, and DNASE1L3) and 6 proteins from sperm cells (acrosome formation-associated factor isoform 2, annexin A1, disintegrin and metalloproteinase domain-containing protein 2, dihydrolipoyl dehydrogenase, and glyceraldehyde-3-phosphate dehydrogenase) were highly expressed ( < 0.05) in the high freezability group. Another 6 seminal plasma proteins (acrosin inhibitor 1, glutathione peroxidase 3, metalloproteinase inhibitor 2, ephrin-A1, annexin A1, and platelet-activating factor acetylhydrolase) were significantly higher ( < 0.05) in the low freezability group. We described the associations of seminal plasma and sperm cell proteins with post-thawing sperm viability of Guzerat bulls raised in a typical semiarid environment. Such associations indicate that specific seminal plasma proteins more abundant in bulls of low semen freezability may be a response to an early oxidative stress that is not detected by conventional prefreezing semen evaluation. Moreover, specific sperm proteins were more associated with good freezability. The results presented here can serve as guidelines for future research aiming to develop better extenders and/or to improve bull semen selection for cryopreservation.

Rearing system and oleic acid supplementation effect on carcass and lipid characteristics of two muscles from an obese pig breed.

Quality of pork depends on genotype, rearing and pre- and post-slaughter conditions. However, no information is available on rearing system changes and oleic acid supplementation on carcass characteristics and fatty acid (FA) profile of pork from the Alentejano (AL) pig, an obese breed. This study evaluates the effects of feeding low (LO) or high oleic acid diets (HO) to AL pigs reared in individual pens (IND) or outdoor (OUT) with access to pasture. Carcass composition was obtained and longissimus dorsi and semimembranosus samples were collected to analyse chemical composition and neutral and polar intramuscular lipids FA profile by gas chromatography. Statistical analysis was performed by a two-way ANOVA for rearing system and diet effects. OUT-reared pigs presented leaner carcasses than IND-reared ones. Both muscles presented lower intramuscular lipid content in OUT-reared pigs. Treatments affected the FA profile of muscles. Overall, OUT-reared pigs presented lower n-6/n-3 FA ratios, whereas pigs fed the HO diet exhibited lower saturated fatty acids (SFA), higher monounsaturated fatty acids (MUFA) levels and lower thrombogenic indexes on neutral intramuscular lipids than LO-fed pigs. On the polar fraction, OUT-reared pigs presented lower SAT and n-6/n-3 FA ratio, and higher polyunsaturated fatty acids (PUFA) levels on both muscles. Pigs fed the HO diet exhibited higher MUFA and lower PUFA levels on both muscles, and lower SAT levels on semimembranosus. This study shows rearing system and oleic acid supplementation have complementary effects and influence carcass composition and the nutritional quality of meat.

Technical developments of functional electrical stimulation to correct drop foot: sensing, actuation and control strategies.

This work presents a review on the technological advancements over the last decades of functional electrical stimulation based neuroprostheses to correct drop foot. Functional electrical stimulation is a technique that has been put into practice for several years now, and has been shown to functionally restore and rehabilitate individuals with movement disorders, such as stroke, multiple sclerosis and traumatic brain injury, among others. The purpose of this technical review is to bring together information from a variety of sources and shed light on the field's most important challenges, to help in identifying new research directions. The review covers the main causes of drop foot and its associated gait implications, along with several functional electrical stimulation-based neuroprostheses used to correct it, developed within academia and currently available in the market. These systems are thoroughly analyzed and discussed with particular emphasis on actuation, sensing and control of open- and closed-loop architectures. In the last part of this work, recommendations on future research directions are suggested.

Dynamic structure of NGF and proNGF complexed with p75NTR: pro-peptide effect.

Crystallographic structures of NGF/p75NTR and proNGF/p75NTR were previously obtained in 2:1 and 2:2 stoichiometries, respectively. However, evidence shows that both stoichiometries can occur for mature neurotrophins and pro-neurotrophins. We used Molecular Dynamics (MD) simulations to examine the energetic and structural characteristics of these two complete systems as well as the uncomplexed forms of NGF and understand how these could translate in a new view of different biological outcomes. Here, we show that one chain at the 2:2 proNGF complex seems to be preferentially lost creating a 2:1 structure able to interact with sortilin. We also demonstrated that the structure of the neurotrophin dimers is not pre-established and suffers large structural modifications upon p75NTR binding. Moreover, our data suggests an elegant explanation for the dual role of NGF in neuronal cell death and survival, where different stoichiometries induce conformational changes that might be the basis for the different biological outcomes observed with the mature and proforms of neurotrophins.

Application of synchrotron X-ray microtomography for visualizing bacterial biofilms 3D microstructure in porous media.

The development of reliable models to accurately predict biofilm growth in porous media relies on a good knowledge of the temporal evolution of biofilms structure within the porous network. Since little is known on the true 3D structure of biofilms developed in porous media, this work aimed at developing a new experimental protocol to visualize the 3D microstructure of bacterial biofilms in porous media. The main originality of the proposed procedure lies on the combination of the more recent advances in synchrotron microtomography (Paganin mode) and of a new contrast agent (1-chloronaphtalene) that has never been applied to biofilm visualization. It is shown that the proposed methodology takes advantage of the contrasting properties of 1-chloronaphtalene to prevent some limitations observed with more classical contrast agents. A quantitative analysis of the microstructural properties (volume fractions and specific surface area) of bacterial biofilms developed in columns of clay beads is also proposed on the basis of the obtained 3D images.

Ligand-induced structural changes in TEM-1 probed by molecular dynamics and relative binding free energy calculations.

The TEM family of enzymes has had a crucial impact on the pharmaceutical industry due to their important role in antibiotic resistance. Even with the latest technologies in structural biology and genomics, no 3D structure of a TEM-1/antibiotic complex is known previous to acylation. Therefore, the comprehension of their capability in acylate antibiotics is based on the protein macromolecular structure uncomplexed. In this work, molecular docking, molecular dynamic simulations, and relative free energy calculations were applied in order to get a comprehensive and thorough analysis of TEM-1/ampicillin and TEM-1/amoxicillin complexes. We described the complexes and analyzed the effect of ligand binding on the overall structure. We clearly demonstrate that the key residues involved in the stability of the ligand (hot-spots) vary with the nature of the ligand. Structural effects such as (i) the distances between interfacial residues (Ser70-Oγ and Lys73-Nζ, Lys73-Nζ and Ser130-Oγ, and Ser70-Oγ-Ser130-Oγ), (ii) side chain rotamer variation (Tyr105 and Glu240), and (iii) the presence of conserved waters can be also influenced by ligand binding. This study supports the hypothesis that TEM-1 suffers structural modifications upon ligand binding.