Agreement between mechanical and digital skinfold callipers.

Background: Skinfold callipers are often used in clinical practice to estimate subcutaneous adipose tissue thickness. Recently, LipoTool emerged as a potential digital system to measure skinfolds, however comparisons with competing equipment are lacking. Aim: The aim of this study was to test the agreement between two competing skinfold callipers (digital and mechanical). Methods: The sample included 22 healthy male adult participants. A certified observer measured eight skinfolds twice using different skinfold callipers (digital and mechanical). Differences between equipment were tested using Wilcoxon signed rank test The distribution of error was examined using the normality test Results: Differences between skinfold callipers were significantly in five skinfolds: triceps (Z = -3.546; P < 0.001), subscapular (Z = -3.984; P < 0.001), suprailiac (Z = 3.024; P = 0.002), supraspinale (Z = 3.885; P < 0.001), abdominal (Z z = -2.937; P = 0.003), thigh (Z = -2.224; P = 0.026) and calf (Z = -2.052; P = 0.040). Differences between callipers were constant. Conclusions: Mechanical and digital callipers tended to record different values of skinfold thickness. Clinical examination should consider equipment-related variation in fat mass estimation.

Multiple keratotic projections on the palms and soles.

Spiny keratoderma (SKD) is a rare palmoplantar keratoderma that presents with few to numerous millimetric hyperkeratotic projections on the palms and soles. It has been described with both hereditary and acquired variants. The acquired form, which presents in older adults, has been associated with a variety of systemic diseases and malignant conditions. In patients suspected of having acquired spiny keratoderma, an evaluation for malignant conditions may be warranted. Treatment with topical keratolytics or topical and oral retinoids is usually insufficient. Herein, we present the case of a 58-year-old man diagnosed with idiopathic SKD.

Crystallographic approach to fragment-based hit discovery against Schistosoma mansoni purine nucleoside phosphorylase.

Several Schistosoma species cause Schistosomiasis, an endemic disease in 78 countries that is ranked second amongst the parasitic diseases in terms of its socioeconomic impact and human health importance. The drug recommended for treatment by the WHO is praziquantel (PZQ), but there are concerns associated with PZQ, such as the lack of information about its exact mechanism of action, its high price, its effectiveness - which is limited to the parasite's adult form - and reports of resistance. The parasites lack the de novo purine pathway, rendering them dependent on the purine salvage pathway or host purine bases for nucleotide synthesis. Thus, the Schistosoma purine salvage pathway is an attractive target for the development of necessary and selective new drugs. In this study, the purine nucleotide phosphorylase II (PNP2), a new isoform of PNP1, was submitted to a high-throughput fragment-based hit discovery using a crystallographic screening strategy. PNP2 was crystallized and crystals were soaked with 827 fragments, a subset of the Maybridge 1000 library. X-ray diffraction data was collected and structures were solved. Out of 827-screened fragments we have obtained a total of 19 fragments that show binding to PNP2. Fourteen of these fragments bind to the active site of PNP2, while five were observed in three other sites. Here we present the first fragment screening against PNP2.

Dissecting protein domain variability in the core RNA interference machinery of five insect orders.

RNA interference (RNAi)-mediated gene silencing can be used to control specific insect pest populations. Unfortunately, the variable efficiency in the knockdown levels of target genes has narrowed the applicability of this technology to a few species. Here, we examine the current state of knowledge regarding the miRNA (micro RNA) and siRNA (small interfering RNA) pathways in insects and investigate the structural variability at key protein domains of the RNAi machinery. Our goal was to correlate domain variability with mechanisms affecting the gene silencing efficiency. To this end, the protein domains of 168 insect species, encompassing the orders Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera, were analysed using our pipeline, which takes advantage of meticulous structure-based sequence alignments. We used phylogenetic inference and the evolutionary rate coefficient (K) to outline the variability across domain regions and surfaces. Our results show that four domains, namely dsrm, Helicase, PAZ and Ribonuclease III, are the main contributors of protein variability in the RNAi machinery across different insect orders. We discuss the potential roles of these domains in regulating RNAi-mediated gene silencing and the role of loop regions in fine-tuning RNAi efficiency. Additionally, we identified several order-specific singularities which indicate that lepidopterans have evolved differently from other insect orders, possibly due to constant coevolution with plants and viruses. In conclusion, our results highlight several variability hotspots that deserve further investigation in order to improve the application of RNAi technology in the control of insect pests.

Stakeholder views of source separation collection programme in East São Paulo, Brazil.

The investigation of the views of the stakeholders involved in the municipal solid waste separate collection programme (CP) performed in the East Zone of the city of São Paulo is presented in this paper. Aiming to obtain the necessary information to be analysed, interviews with the manager of the Municipal Urban Cleaning Authority (MUCA) of the city, with leaders of recycling worker cooperatives (WCs), and citizens were performed using semi-structured questionnaires. The analysis was performed using the software "IRAMUTEQ". The results show that, in the view of the manager of the MUCA of the city and the WCs' leaders, the low adhesion of the population to the separate CP is the greatest obstacle to a further expansion of the existing programme. At the same time, the citizens have blamed the low diffusion made by the municipality about the separate CP in the East Zone of São Paulo. Thus, it can be concluded that the separate CP available in the East Zone of São Paulo is still flawed; since neither the public power, the WCs, nor the population are satisfied and point out several flaws. This situation highlights the need to establish better venues for discussion between the population, WCs, and the municipality to jointly design a separate collection system with a more participatory approach.

The structure of the extended E2 DNA-binding domain of the bovine papillomavirus-1.

Bovine papillomavirus proteins were extensively studied as a prototype for the human papillomavirus. Here, the crystal structure of the extended E2 DNA-binding domain of the dominant transcription regulator from the bovine papillomavirus strain 1 is described in the space group P31 21. We found two protein functional dimers packed in the asymmetric unit. This new protein arrangement inside the crystal led to the reduction of the mobility of a previously unobserved loop directly involved in the protein-DNA interaction, which was then modeled for the first time.

Oceans of stimuli: an individual-based model to assess the role of olfactory cues and local enhancement in seabirds' foraging behaviour.

Oceans are extremely dynamic environments, which poses challenges for top-predators such as seabirds to find food resources. Yet, seabirds evolved sensorial abilities (olfactory senses) along with complex behaviours (social information transfer through local enhancement) to improve foraging efficiency. Using the Cory's shearwater (Calonectris borealis) as a model species, we developed an individual-based model to explore the complementary role of different searching mechanisms (olfactory foraging and local enhancement) for the optimal foraging behaviour of pelagic seabirds during 1-day foraging trips around breeding colonies. Model outputs were compared with observed patterns of Cory's shearwaters distribution during local foraging trips. Also, the foraging efficiency of virtual individuals was analysed considering hypothetical scenarios of foraging conditions and densities of foraging individuals around breeding colonies. The results support the use of a combination of searching strategies by Cory's shearwaters, which produced representative patterns of space use from tracked individuals, including spatial foraging segregation of neighbouring sub-colonies. Furthermore, while the mechanisms underpinning local enhancement played a key role in mitigating sub-optimal foraging conditions, the use of olfactory senses conferred great adaptive foraging advantages over a wide range of environmental conditions. Our results also indicate a synergistic effect between the two strategies, which suggests that a multimodal foraging strategy is useful to forage in extremely dynamic environments. The developed model provides a basis for further investigation regarding the role of foraging mechanisms in the population dynamics of colonial animals, including the adaptive foraging behaviour of marine top predators to dynamic environmental conditions.

Use of construction and demolition solid wastes for basket gabion filling.

Construction and demolition wastes have been studied by technical means aiming at the development of management tools to reduce their environmental impacts. Among these, recycling can be highlighted. This paper aims at the technical assessment of basket gabions filled with construction and demolition solid waste. Gabions are usually used for retaining walls construction, and these are commonly filled with rocks. Retaining walls are essential for earthfill slopes stabilization, and they must have proper characteristics of strength. However, depending on the slope height or the technical responsibility of the retaining wall, alternative materials with proper characteristics could be used to fill the gabions. The use of recycled material for gabion filling could reduce environmental impacts and costs caused by retaining wall construction. So, basket gabion cells were filled with construction solid waste and basaltic rocks, both crushed into coarse granulometry aiming to compare technical characteristics among them. The performed laboratory tests showed that the horizontal and vertical displacements determined for gabion filled with wastes were near to those obtained for gabions filled with basaltic rocks for a retaining wall of 5 m and up. In conclusion, it can be drawn that basket gabions filled with construction and demolition waste may be a technical alternative for civil construction, reducing environmental impacts and raw material consumption for retaining wall execution.

Crystallographic structure of a complex between trypsin and a nonapeptide derived from a Bowman-Birk inhibitor found in Vigna unguiculata seeds.

Natural inhibitors of proteases have been classified into different families, among them is the Bowman-Birk Inhibitor (BBI) family. Members of BBI have two structurally reactive loops that simultaneously inhibit trypsin and chymotrypsin. Here, we have investigated the binding of bovine trypsin by a cyclic nonapeptide, named PTRY9 (CTKSIPPQC), derived of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) from Vigna unguiculata seeds. This peptide was synthetically produced with the disulfide bond restraining its conformation to mimic the reactive loop that inhibits trypsin. PTRY9 complexed to pancreatic bovine trypsin was crystallized in orthorhombic and trigonal space groups, P212121 and P3221, with maximum resolutions of 1.15 and 1.61 Å, respectively. The structures presented refinement parameters of Rwork = 14.52 % and Rfree = 15.59 %; Rwork = 15.60 % and Rfree = 18.78 %, and different surface area between the peptide and the enzyme of 1024 Å2 and 1070 Å2, respectively. The binding site of the PTRY9 is similar to that found for BTCI as shown by a r.m.s.d. of 0.358 Šbetween the superimposed structures and the electrostatic complementary pattern at the enzyme-peptide interface. Additionally, enzyme inhibition assays show that the affinity of trypsin for PTRY9 is smaller than that for BTCI. In vitro assays revealed that, like BTCI, this synthetic peptide is not cytotoxic for normal mammary epithelial MCF-10A cells, but exerts cytotoxic effects on MDA.MB.231 invasive human breast cancer cells.

Is wind energy increasing the impact of socio-ecological change on Mediterranean mountain ecosystems? Insights from a modelling study relating wind power boost options with a declining species.

The growing concern about future challenges of energy security and climate change has led to the expansion of renewable energy production, with a special emphasis on wind power. Despite the environmental advantages of wind power, it's important to assess the impacts caused by the presence of wind farms on wildlife, particularly on species also affected by habitat loss and degradation. In Mediterranean Europe, the skylark (Alauda arvensis) is a declining passerine that breeds in mountain habitats vulnerable to the abandonment of traditional management practices and climate change. We have created a spatially explicit agent-based model (ABM) in order to replicate the selection of territories, evaluating the effect of wind farms on the mortality rate of breeding males. We were especially interested in assessing the mortality rates related with the interplay between habitat loss due to socio-ecological change and increasing wind power using alternative strategies: adding wind turbines or substituting existing wind turbines by more powerful ones, i.e. repowering. Several known aspects related with the risk of collision of A. arvensis with wind turbines were considered, particularly regarding the male habitat selection and behaviour displayed throughout the breeding season. By simulating a sequential contraction of suitable habitat for the species, we found a substantial increase in the breeding territories superimposed to the wind farm influence zone. In these conditions males' relative mortality was predicted to suffer significant increases. For equivalent wind power, adding wind turbines produced significant increases in the males' relative mortality, whereas repowering didn't. Based on our findings we propose repowering as a defensible strategy to increase wind energy production without increasing A. arvensis collision risk. We highlight that this strategy might also benefit other vulnerable bird and bat species associated with declining habitats of mountain ridges in the Mediterranean region.

Physiological response, antioxidant enzyme activities and conservation of banana treated with ethanol vapor.

Ethanol can inhibit ethylene and retard decay of several fruit. However, the effect of ethanol on ethylene and oxidative stress has not yet been observed in bananas. In this work, the effect of ethanol (vapor phase) on physiology and conservation of the banana cv. 'Prata' was investigated. Initially, a group of bananas was analyzed during 8 h of exposure to ethanol, and then another group of bananas was exposed to ethanol for 4 h and then analyzed during 12 days of storage. Ethanol and ethylene concentrations, respiration rate, superoxide dismutase and catalase activities, physico-chemical characteristics and fruit decay were evaluated. Ethanol reduced ethylene production and respiration rate of the banana only when it reached 4 h of exposure, and this was associated with a maximum absorption of ethanol in the fruit peel. Ethanol increased superoxide dismutase and catalase activities from fruit peel only in the first 2 h of exposure to ethanol, i.e. ethanol did not generate significant oxidative stress. During storage, ethanol inhibited ethylene production and was also able to delay fruit decay, but it was not able to influence the respiration rate, conversion of sugars, and fresh weight loss of the fruits. This study showed that ethanol vapor has an inhibitory effect on ethylene metabolism, but it has no potential to control post-harvest ripening of the banana cv. 'Prata'. On the other hand, ethanol delays decay, and this extends fruit shelf life, which is commercially advantageous.

Structural and functional characterization of a novel lipolytic enzyme from a Brazilian Cerrado soil metagenomic library.

OBJECTIVE: To isolate putative lipase enzymes by screening a Cerrado soil metagenomic library with novel features. RESULTS: Of 6720 clones evaluated, Clone W (10,000 bp) presented lipolytic activity and four predicted coding sequences, one of them LipW. Characterization of a predicted esterase/lipase, LipW, showed 28% sequence identity with an arylesterase from Pseudomonas fluorescens (pdb|3HEA) from protein database (PDB). Phylogenetic analysis showed LipW clustered with family V lipases; however, LipW was clustered in different subclade belonged to family V, suggesting a different subgroup of family V. In addition, LipW presented a difference in family V GH motif, a glycine replaced by a serine in GH motif. Estimated molecular weight and stokes radius values of LipW were 29,338.67-29,411.98 Da and 2.58-2.83 nm, respectively. Optimal enzyme activity was observed at pH 9.0-9.5 and at 40 °C. Circular dichroism analysis estimated secondary structures percentages as approximately 45% α-helix and 15% ß-sheet, consistent with the 3D structure predicted by homology. CONCLUSION: Our results demonstrate the isolation of novel family V lipolytic enzyme with biotechnological applications from a metagenomic library.

Homology modeling and molecular dynamics provide structural insights into tospovirus nucleoprotein.

BACKGROUND: Tospovirus is a plant-infecting genus within the family Bunyaviridae, which also includes four animal-infecting genera: Hantavirus, Nairovirus, Phlebovirus and Orthobunyavirus. Compared to these members, the structures of Tospovirus proteins still are poorly understood. Despite multiple studies have attempted to identify candidate N protein regions involved in RNA binding and protein multimerization for tospovirus using yeast two-hybrid systems (Y2HS) and site-directed mutagenesis, the tospovirus ribonucleocapsids (RNPs) remains largely uncharacterized at the molecular level and the lack of structural information prevents detailed insight into these interactions. RESULTS: Here we used the nucleoprotein structure of LACV (La Crosse virus-Orthobunyavirus) and molecular dynamics simulations to access the structure and dynamics of the nucleoprotein from tospovirus GRSV (Groundnut ringspot virus). The resulting model is a monomer composed by a flexible N-terminal and C-terminal arms and a globular domain with a positively charged groove in which RNA is deeply encompassed. This model allowed identifying the candidate amino acids residues involved in RNA interaction and N-N multimerization. Moreover, most residues predicted to be involved in these interactions are highly conserved among tospoviruses. CONCLUSIONS: Crucially, the interaction model proposed here for GRSV N is further corroborated by the all available mutational studies on TSWV (Tomato spotted wilt virus) N, so far. Our data will help designing further and more accurate mutational and functional studies of tospovirus N proteins. In addition, the proposed model may shed light on the mechanisms of RNP shaping and could allow the identification of essential amino acid residues as potential targets for tospovirus control strategies.

Crystal structure of VapC21 from Mycobacterium tuberculosis at 1.31 Å resolution.

Persisters are individual bacterial cells that exhibit a phenotype characterized by slow growth, low metabolic rate and multidrug tolerance. The processes that drive cells into a persistence state constitute an active but incipient research field, and structural data regarding its components are scarce. The molecular targets of many therapeutic drugs are involved in cell wall synthesis and cell division, and these cellular processes are down-regulated in persister cells, consequently these cells are more likely to survive antibiotic treatment. Toxin-antitoxin systems were shown to have a leading role in the formation of persisters, and several pathogenic bacteria display a wide array of these systems. The Mycobacterium tuberculosis H37Rv genome presents 88 toxin-antitoxin loci, of which 47 code for members of the VapBC protein family. To date, only four crystal structures of Mycobacterium tuberculosis VapBC complexes are available, and all of them present the toxin bound to and inhibited by the antitoxin. We present the 1.31 Å resolution structure of VapC21, the first structure of a Mycobacterium tuberculosis VapC toxin in the absence of its cognate inhibitory antitoxin. Our data show that VapC21 is a dimer in solution, with conserved active site architecture and an extensive antitoxin binding groove. Additionally, the strategy used to mutate a putative catalytic residue allowing the expression and purification of soluble VapC21 will pave the way for the resolution of more toxin structures in the absence of antitoxins. Taken together, our findings represent an important step in unraveling the molecular mechanisms related to persistence, which will contribute for the design of faster and more efficient therapeutic approaches for the treatment of tuberculosis, particularly for infections with multidrug-resistant strains.

Combined Use of Ex Vivo Dermoscopy and Histopathology for the Diagnosis of Melanocytic Tumors.

Dermoscopy can be applied to fixed tissues, and dermoscopic patterns correlate with microscopic findings. Data on the influence of ex vivo dermoscopy on pathologic diagnosis of melanocytic lesions are limited. Therefore, we aimed to determine whether this technique could aid on the histopathological evaluation of melanocytic neoplasms. Sequential cutaneous excisional biopsies of melanocytic lesions and their corresponding ex vivo dermoscopic images were prospectively analyzed. Additional sectioning was executed in areas of dermoscopic concern, having, by reference, a dermoscopic mapping of the sectioned specimens. Diagnostic differences before and after analyzing the new dermoscopy-guided sections were registered. A total of 564 melanocytic lesions were examined, and additional cuts were considered necessary in 84 (14.9%) cases. Of these, 11 lesions (13.1%) had a different final diagnosis after dermoscopy-guided specimen sectioning, including 3 lesions that were reclassified as melanomas and 2 melanomas that were restaged. We found that the combined use of ex vivo dermoscopy and histopathology improves clinical-pathological correlation and allows selection of representative areas for sectioning. Altogether, this technique may improve diagnostic confidence and accuracy in the histopathological evaluation of melanocytic lesions.

A redox 2-Cys mechanism regulates the catalytic activity of divergent cyclophilins.

The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism.