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Transforming growth factor (TGF-β1) is a critical profibrotic mediator in chronic lung disease, and there are no specific strategies to mitigate its adverse effects. Activation of TGF-β1 signaling is a multipart process involving ligands, transmembrane receptors, and transcription factors. In addition, an intricate network of adaptor proteins fine-tunes the signaling strength, duration, and activity. Namely, Smad7 recruits growth arrest and DNA damage (GADD34) protein that then interacts with the catalytic subunit of phosphoprotein phosphatase 1 (PP1c) to inactivate TGF-β receptor (TβR)-I and downregulate TGF-β1 signaling. Little is known about how TGF-β1 releases TβR-I from the GADD34-PP1c inhibition to activate its signaling. Transmembrane lemur tyrosine kinase 2 (LMTK2) is a PP1c inhibitor, and our published data showed that TGF-β1 recruits LMTK2 to the cell surface. Here, we tested the hypothesis that TGF-β1 recruits LMTK2 to inhibit PP1c, allowing activation of TβR-I. First, LMTK2 interacted with the TGF-β1 pathway in the human bronchial epithelium at multiple checkpoints. Second, TGF-β1 inhibited PP1c by an LMTK2-dependent mechanism. Third, TGF-β1 used LMTK2 to activate canonical Smad3-mediated signaling. We propose a model whereby the LMTK2-PP1c and Smad7-GADD34-PP1c complexes serve as on-and-off switches in the TGF-β1 signaling in human bronchial epithelium. NEW & NOTEWORTHY Activation of the transforming growth factor (TGF)-β1 signaling pathway is complex, involving many ligands, transmembrane receptors, transcription factors, and modulating proteins. The mechanisms of TGF-β1 signaling activation/inactivation are not fully understood. We propose for the first time a model by which transmembrane lemur tyrosine kinase 2 (LMTK2) forms a complex with phosphoprotein phosphatase 1 (PP1c) to activate TGF-β1 signaling and Smad7, growth arrest and DNA damage (GADD34), and PP1C form a complex to inactivate TGF-β1 signaling in human bronchial epithelium.

Fluorescence-based biosensors have widely been used in the life-sciences and biomedical applications due to their low limit of detection and a diverse selection of fluorophores that enable simultaneous measurements of multiple biomarkers. Recent research effort has been made to implement fluorescent biosensors into the exploding field of point-of-care testing (POCT), which uses cost-effective strategies for rapid and affordable diagnostic testing. However, fluorescence-based assays often suffer from their feeble signal at low analyte concentrations, which often requires sophisticated, costly, and bulky instrumentation to maintain high detection sensitivity. Metal- and metal oxide-based nanostructures offer a simple solution to increase the output signal from fluorescent biosensors due to the generation of high field enhancements close to a metal or metal oxide surface, which has been shown to improve the excitation rate, quantum yield, photostability, and radiation pattern of fluorophores. This article provides an overview of existing biosensors that employ various strategies for fluorescence enhancement via nanostructures and have demonstrated the potential for use as POCT. Biosensors using nanostructures such as planar substrates, freestanding nanoparticles, and metal-dielectric-metal nanocavities are discussed with an emphasis placed on technologies that have shown promise towards POCT applications without the need for centralized laboratories., (© 2022 The Authors. Advanced Materials published by Wiley-VCH GmbH.)

In the plant sciences, results of laboratory studies often do not translate well to the field. To help close this lab-field gap, we developed a strategy for studying the wiring of plant traits directly in the field, based on molecular profiling and phenotyping of individual plants. Here, we use this single-plant omics strategy on winter-type Brassica napus (rapeseed). We investigate to what extent early and late phenotypes of field-grown rapeseed plants can be predicted from their autumnal leaf gene expression, and find that autumnal leaf gene expression not only has substantial predictive power for autumnal leaf phenotypes but also for final yield phenotypes in spring. Many of the top predictor genes are linked to developmental processes known to occur in autumn in winter-type B. napus accessions, such as the juvenile-to-adult and vegetative-to-reproductive phase transitions, indicating that the yield potential of winter-type B. napus is influenced by autumnal development. Our results show that single-plant omics can be used to identify genes and processes influencing crop yield in the field., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 De Meyer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: The current classification for acute kidney injury (AKI) according to the Kidney Disease: Improving Global Outcomes (KDIGO) criteria integrates both serum creatinine (SCr) and urine output (UO). Most reports on AKI claim to use KDIGO guidelines but fail to include the UO criterion. It has been shown that patients who had intensive UO monitoring, with or without AKI, had significantly less cumulative fluid volume and fluid overload, reduced vasopressor use, and improved 30-day mortality. We examined whether real-time monitoring of this simple, sensitive, and easy-to-use biomarker in the ICU led to more appropriate intervention by healthcare providers and better outcomes.  METHODS: RenalSense Clarity RMS Consoles were installed in the General ICU at the Hadassah Medical Center, Israel, from December 2019 to November 2020. The Clarity RMS system continuously and electronically monitors UO in real-time. 100 patients were randomly selected from this period as the study group (UO elec ) and compared to a matched control group (UO manual ) from the same period two years earlier. To test whether there was an association between oliguric hours and fluid treatment in each group, the correlation was calculated and analyzed for each of the different UO monitoring methods., Results: Therapeutic intervention: The correlation of the sum of all oliguric hours on Day 1 and 2 with the sum of any therapeutic intervention (fluid bolus or furosemide) showed a significant correlation for the study group UO elec (P = 0.017). The matched control group UO manual showed no such correlation (P = 0.932). Length of Stay (LOS): Median LOS [IQR] in the ICU of UO elec versus UO manual was 69.46 [44.7, 125.9] hours and 116.5 [62.46, 281.3] hours, respectively (P = 0.0002)., Conclusions: The results of our study strongly suggest that ICU patients had more meaningful and better medical intervention, and improved outcomes, with electronic UO monitoring than with manual monitoring., (© 2022. The Author(s).)

The oral cavity harbors hundreds of microorganisms that may be uncontrolled and provoke several diseases. In this sense, periodontitis is a complex multifactorial disease with an essential microbial component in its etiology. Periodontal treatment involves mechanical control of the supra- and subgingival biofilm, but not all patients respond predictably to treatment. In this way, the biofilm chemical control helps in the reduction of periodontal pathogens during treatment or in the delay of bacterial re-colonization after scaling and root planning. Several products have been studied as adjunctive therapy and have shown promising results. Therefore, the present article reviews the biological effects of propolis, aloe vera, green tea, cranberry, calendula, myrrha and salvia that may support their use in the control of subgingival biofilm in patients with periodontitis. All the natural products cited above showed exciting results against microorganisms related to oral diseases, mainly periodontitis. These substances also have anti-inflammatory and antioxidant activities. The natural agents propolis, aloe vera, green tea, cranberry, calendula, myrrha and salvia demonstrated potential to be used as oral hygiene products, based on their antimicrobial and anti-inflammatory actions.

Controlled drug delivery systems can provide sustained release profiles, favorable pharmacokinetics, and improved patient adherence. Here, a reservoir-style implant comprising a biodegradable polymer, poly(ε-caprolactone) (PCL), was developed to deliver drugs subcutaneously. This work addresses a key challenge when designing these implantable drug delivery systems, namely the accurate prediction of drug release profiles when using different formulations or form factors of the implant. The ability to model and predict the release behavior of drugs from an implant based on their physicochemical properties enables rational design and optimization without extensive and laborious in vitro testing. By leveraging experimental observations, we propose a mathematical model that predicts the empirical parameters describing the drug diffusion and partitioning processes based on the physicochemical properties of the drug. We demonstrate that the model enables an adequate fit predicting empirical parameters close to experimental values for various drugs. The model was further used to predict the release performance of new drug formulations from the implant, which aligned with experimental results for implants exhibiting zero-order release kinetics. Thus, the proposed empirical models provide useful tools to inform the implant design to achieve a target release profile.

We report the largest and most diverse genetic study of type 1 diabetes (T1D) to date (61,427 participants), yielding 78 genome-wide-significant (P < 5 × 10 -8 ) regions, including 36 that are new. We define credible sets of T1D-associated variants and show that they are enriched in immune-cell accessible chromatin, particularly CD4 + effector T cells. Using chromatin-accessibility profiling of CD4 + T cells from 115 individuals, we map chromatin-accessibility quantitative trait loci and identify five regions where T1D risk variants co-localize with chromatin-accessibility quantitative trait loci. We highlight rs72928038 in BACH2 as a candidate causal T1D variant leading to decreased enhancer accessibility and BACH2 expression in T cells. Finally, we prioritize potential drug targets by integrating genetic evidence, functional genomic maps and immune protein-protein interactions, identifying 12 genes implicated in T1D that have been targeted in clinical trials for autoimmune diseases. These findings provide an expanded genomic landscape for T1D., (© 2021. Crown.)

Ebola virus (EBOV) hemorrhagic fever outbreaks have been challenging to deter due to the lack of health care infrastructure in disease-endemic countries and a corresponding inability to diagnose and contain the disease at an early stage. EBOV vaccines and therapies have improved disease outcomes, but the advent of an affordable, easily accessed, mass-produced rapid diagnostic test (RDT) that matches the performance of more resource-intensive polymerase chain reaction (PCR) assays would be invaluable in containing future outbreaks. Here, we developed and demonstrated the performance of a new ultrasensitive point-of-care immunoassay, the EBOV D4 assay, which targets the secreted glycoprotein of EBOV. The EBOV D4 assay is 1000-fold more sensitive than the U.S. Food and Drug Administration-approved RDTs and detected EBOV infection earlier than PCR in a standard nonhuman primate model. The EBOV D4 assay is suitable for low-resource settings and may facilitate earlier detection, containment, and treatment during outbreaks of the disease., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Lemur tyrosine kinase 2 (LMTK2) is a transmembrane Ser/Thr kinase whose role has been increasingly recognized; however, when compared to other kinases, understanding of the LMTK2 networks and biological functions is still limited. Recent data have shown that transforming growth factor (TGF)-β1 plays a role in modulating LMTK2 function by controlling its endocytic trafficking in human bronchial epithelial cells. Here, we aimed to unveil the LMTK2 regulatory network and elucidate how it affects cellular functions and disease pathways in either TGF-β1 dependent or independent manner. To understand how the LMTK2 and TGF-β1 pathways interconnect, we knocked down (KD) LMTK2 using small(si)RNA-mediated silencing in human bronchial epithelial CFBE41o- cells, treated cells with TGF-β1 or vehicle control, and performed differential gene expression analysis by RNA sequencing (RNAseq). In vehicle-treated cells, LMTK2 KD affected expression of 2,506 genes while it affected 4,162 genes after TGF-β1 stimulation. Bioinformatics analysis shows that LMTK2 is involved in diverse cellular functions and disease pathways, such as cell death and survival, cellular development, and cancer susceptibility. In summary, our study increases current knowledge about the LMTK2 network and its intersection with the TGF-β1 signaling pathway. These findings will serve as basis for future exploration of the predicted LMTK2 interactions and signaling pathways., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Cruz, Mitash, Mu, Farinha and Swiatecka-Urban.)

Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap., (© 2020 The Authors. Published under the terms of the CC BY 4.0 license.)

Fluorescence-based microarrays are promising diagnostic tools due to their high throughput, small sample volume requirements, and multiplexing capabilities. However, their low fluorescence output has limited their implementation for in vitro diagnostics applications in point-of-care (POC) settings. Here, by integration of a sandwich immunoassay microarray within a plasmonic nanogap cavity, we demonstrate strongly enhanced fluorescence which is critical for readout by inexpensive POC detectors. The immunoassay consists of inkjet-printed antibodies on a polymer brush which is grown on a gold film. Colloidally synthesized silver nanocubes are placed on top and interact with the underlying gold film creating high local electromagnetic field enhancements. By varying the thickness of the brush from 5 to 20 nm, up to a 151-fold increase in fluorescence and 14-fold improvement in the limit-of-detection is observed for the cardiac biomarker B-type natriuretic peptide (BNP) compared to the unenhanced assay, paving the way for a new generation of POC clinical diagnostics.

The most common disease-causing mutation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene, F508del, leads to cystic fibrosis (CF), by arresting CFTR processing and trafficking to the plasma membrane. The FDA-approved modulators partially restore CFTR function and slow down the progression of CF lung disease by increasing processing and delivery to the plasma membrane and improving activity of F508del-CFTR Cl - channels. However, the modulators do not correct compromised membrane stability of rescued F508del-CFTR. Transforming growth factor (TGF)-β1 is a well-established gene modifier of CF associated with worse lung disease in F508del-homozygous patients, by inhibiting CFTR biogenesis and blocking the functional rescue of F508del-CFTR. Lemur tyrosine kinase 2 (LMTK2) is a transmembrane protein localized at the apical and basolateral membrane domain of human bronchial epithelial cells. Phosphorylation of the apical membrane CFTR by LMTK2 triggers its endocytosis and reduces the abundance of membrane-associated CFTR, impairing the CFTR-mediated Cl - transport. We have previously shown that LMTK2 knockdown improves the pharmacologically rescued F508del-CFTR abundance and function. Thus, reducing the LMTK2 recruitment to the plasma membrane may provide a useful strategy to potentiate the pharmacological rescue of F508del-CFTR. Here, we elucidate the mechanism of LMTK2 recruitment to the apical plasma membrane in polarized CFBE41o- cells. TGF-β1 increased LMTK2 abundance selectively at the apical membrane by accelerating its recycling in Rab11-positive vesicles without affecting LMTK2 mRNA levels, protein biosynthesis, or endocytosis. Our data suggest that controlling TGF-β1 signaling may attenuate recruitment of LMTK2 to the apical membrane thereby improving stability of pharmacologically rescued F508del-CFTR., (Copyright © 2020 Cruz, Mitash, Farinha and Swiatecka-Urban.)

Purpose This study examines the utility of Video-Implemented Script Training for Aphasia (VISTA) for improving speech production and fluency in a Spanish-English bilingual speaker with aphasia. Method In this single-subject, multiple-baseline intervention study, VISTA was utilized to facilitate fluent and intelligible speech through training with an audiovisual speech model. Scripts were developed from personalized topics of interest, and training stimuli were tailored for speech rate and linguistic complexity. One trained script per language contained a high proportion of cognates in order to examine the potential for enhancing cross-linguistic transfer. Primary and secondary outcome measures for trained and untrained scripts were percent correct and intelligible scripted words, grammatical errors, speech rate, and total percent intelligibility. Results R. C. showed significant improvement in accuracy, intelligibility, and grammaticality of trained scripts. Results revealed cross-linguistic transfer for both languages of treatment. A significantly greater magnitude of cross-language transfer was observed for scripts that were not cognate dense. Conclusions VISTA is a viable treatment method for bilingual individuals with aphasia. Cross-linguistic transfer was diminished when incorporating scripts with a high proportion of cognates; however, this may not be true for all bilingual individuals with aphasia and should be explored with additional participants.

Objective: This study assessed the impact of chronic periodontitis (CP) and CP associated with type 2 diabetes mellitus (DM) and/or smoking on the serum ratios of pro- to anti-inflammatory cytokines., Materials and Methods: Subjects were assigned into one of the following groups: control (n = 25, non-diabetic non-smokers with no history of periodontitis), CP (n = 26, non-diabetic non-smokers with CP), DMCP (n = 30, non-smokers with DM and CP), SCP (n = 27, non-diabetic smokers with CP), and SDMCP (n = 22, smokers with type 2 DM and CP). Serum levels of 18 cytokines were measured using multiplex immunoassays., Results: Six ratios of pro-inflammatory to anti-inflammatory cytokines were significantly higher in the CP group than in the control group (p < 0.05). Eleven, seventeen and nine ratios of pro-inflammatory to anti-inflammatory cytokines were significantly higher in the DMCP, SCP and SDMCP groups than in the control group, respectively (p < 0.05). The SCP group presented higher serum ratios of tumor necrosis factor (TNF)-α/interleukin (IL)-4, TNF-α/IL-5, IL-17/IL-13 and IL-6/IL-13 (p < 0.05) than the CP group. Cluster analysis revealed a relevant cluster composed of ten cytokines (IL-17, IL-23, interferon-γ, IL-12, IL-1β, IL-2, IL-21, IL-6, IL-4 and granulocyte-macrophage colony-stimulating factor [GM-CSF]) in the serum of subjects from the DMCP group., Conclusions: The ratios of pro- to anti-inflammatory cytokines shift to favor a pro-inflammatory status in the serum of patients with CP and even more when CP is associated with one or both risk factors., Clinical Relevance: CP and CP associated with hyperglycemia and/or smoking might contribute to a systemic inflammatory burden and increased risk of systemic complications.

Lemur Tyrosine Kinase 2 (LMTK2) is a recently cloned transmembrane protein, actually a serine/threonine kinase named after the Madagascar primate lemur due to the long intracellular C-terminal tail. LMTK2 is relatively little known, compared to other kinases but its role has been increasingly recognized. Published data show that LMTK2 regulates key cellular events, including endocytic trafficking, nerve growth factor signaling, apoptosis, and Cl - transport. Abnormalities in the expression and function of LMTK2 are associated with human disease, such as neurodegeneration, cancer and infertility. We summarized the current state of knowledge on LMTK2 structure, regulation, interactome, intracellular localization, and tissue expression and point out future research directions to better understand the role of LMTK2.

Aim: This study evaluated the levels of sclerostin (SOST) and Dickkopf (DKK)-1 in the chronic periodontitis (CP) associated with type 2 diabetes (DM) and/or smoking. Relationships between SOST, DDK1, RANKL, OPG, IL-1ß, IL-6 and TNF-α, and pathogens were assessed., Material and Methods: The study population included non-diabetic non-smokers (control), non-smokers with DM (DM group), non-diabetic smokers (S group) and smokers with DM (SDM group), all with CP. Serum and gingival levels of SOST, DKK1, RANKL, OPG, IL-1ß, IL-6 and TNF-α were evaluated by multiplex immunoassay. Gene expressions of these biomarkers and subgingival levels of pathogens were assessed by qPCR., Results: Gingival protein and/or mRNA levels of DKK1 and SOST were higher in subjects with DM and/or smoking than in controls (p < .05). Serum levels of SOST were higher in the DM group than in controls (p < .05). DKK1 positively correlated with SOST in the DM, SDM and control groups (p < .05) at mRNA levels. DKK-1 and SOST correlated with pathogens, especially in both groups with DM., Conclusions: SOST and DKK1 were upregulated in patients with CP presenting DM and/or smoking. DM, alone or with smoking, particularly influenced the correlations of SOST and DKK1 with each other and with the other biomarkers mostly at mRNA levels, as well as with periodontal pathogens., (© 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Objective: To evaluate the effects of metformin on bone healing around titanium implants inserted in non-diabetic rats., Methods: Twenty Wistar rats were randomly assigned to one of the following groups: control group (n = 10): rats without metformin treatment; MT group (n = 10): rats treated with metformin (40 mg/kg/day by gavage). At thirty days after implant placement, animals were euthanized. Histometric measurements of bone-to-implant contact (BIC) and bone area (BA), in addition to immunohistochemical analysis of the number of cells stained for RANKL and OPG, were assessed in the cortical and medullary areas around implants., Results: The percentages of BIC and BA in the cortical bone were significantly lower in the MT group than in the control group (P < 0.05). Furthermore, the medullary bone around the implants inserted in the metformin-treated animals exhibited an increased number of RANKL-stained cells than that around the implants inserted in the control animals (P < 0.05)., Conclusions: Metformin negatively affected osseointegration by reducing the percentages of BIC and BA and increasing the expression of RANKL around titanium implants inserted in non-diabetic rats., (© 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

The coating of fertilizers with polymers is an acknowledged strategy for controlling the release of nutrients and their availability in soil. However, its effectiveness in the case of soluble phosphate fertilizers is still uncertain, and information is lacking concerning the chemical properties and structures of such coatings. Here, an oil-based hydrophobic polymer system (polyurethane) is proposed for the control of the release of phosphorus from diammonium phosphate (DAP) granules. This material was systematically characterized, with evaluation of the delivery mechanism and the availability of phosphate in an acid soil. The results indicated that thicker coatings can change the maximum nutrient availability toward longer periods, such as 4.5-7.5 wt % DAP coated, that presented the highest concentrations at 336 h, as compared to 168 h for uncoated DAP. In contrast, DAP treated with 9.0 wt % began to increase the concentration after 168 h until it results in maximum release at 672 h. These effects could be attributed to the homogeneity of the polymer and the porosity. The strategy successfully provided long-term availability of a phosphate source.

Hard spheres are an important benchmark of our understanding of natural and synthetic systems. In this work, colloidal experiments and Monte Carlo simulations examine the equilibrium and out-of-equilibrium assembly of hard spheres of diameter σ within cylinders of diameter σ≤D≤ 2.82σ. Although phase transitions formally do not exist in such systems, marked structural crossovers can nonetheless be observed. Over this range of D, we find in simulations that structural crossovers echo the structural changes in the sequence of densest packings. We also observe that the out-of-equilibrium self-assembly depends on the compression rate. Slow compression approximates equilibrium results, while fast compression can skip intermediate structures. Crossovers for which no continuous line-slip exists are found to be dynamically unfavorable, which is the main source of this difference. Results from colloidal sedimentation experiments at low diffusion rate are found to be consistent with the results of fast compressions, as long as appropriate boundary conditions are used.

Purpose: There is interest in establishing hypoglycemiant agents able to contain/revert the impact of diabetes mellitus on osseointegration. The purpose of this study was to assess the possible effect of metformin in reversing the negative effects of hyperglycemia on the healing of bone surrounding implants inserted in rats., Materials and Methods: Rats (10 per group) were assigned to one of the following groups: DM group: type 2 diabetic rats deprived of metformin (M) treatment; MDM group: type 2 diabetic rats under M treatment (40 mg/kg/day, starting on the 15th day after implant placement); control group: nondiabetic rats without M treatment. At 30 days after streptozotocin injection, titanium implants were placed in tibiae. Animals were euthanized 30 days after implant surgery. Bone-to-implant contact (BIC), bone area (BA), and the number of receptor activator of nuclear factor κB ligand (RANKL)- and osteoprotegerin (OPG)-stained cells were assessed in cortical and medullary areas., Results: The percentages of BIC and BA in the cortical bone were reduced in the DM and MDM groups compared with the control group (P < .05). The percentage of BA in the medullary region was reduced in the DM group compared with the control group (P < .05). The MDM group showed the greatest number of OPG-stained cells, while the DM group presented the greatest ratio of RANKL/OPG in the medullary area (P < .05)., Conclusion: Metformin did not modulate the damaging effect of hyperglycemia on bone healing around implants at histometric levels, but increased the expression of OPG and decreased the RANKL/OPG ratio in the medullary area, yielding some molecular benefits in the osseointegration of implants under the hyperglycemic state.

Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice ( O. sativa ). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several genes controlling panicle architecture and NSP in rice have been identified, there is little evidence of (i) the genetic control of panicle architecture and NSP in different environments and (ii) the presence of stable genetic associations with panicle architecture across environments. This study combines image phenotyping of 225 accessions belonging to a genetic diversity array of indica rice grown under irrigated field condition in two different environments and Genome Wide Association Studies (GWAS) based on the genotyping of the diversity panel, providing 83,374 SNPs. Accessions sown under direct seeding in one environement had reduced Panicle Length (PL), NSP, PBN, PBL, SBN, and SBL compared to those established under transplanting in the second environment. Across environments, NSP was significantly and positively correlated with PBN, SBN and PBL. However, the length of branches (PBL and SBL) was not significantly correlated with variables related to number of branches (PBN and SBN), suggesting independent genetic control. Twenty- three GWAS sites were detected with P ≤ 1.0E-04 and 27 GWAS sites with p ≤ 5.9E-04. We found 17 GWAS sites related to NSP, 10 for PBN and 11 for SBN, 7 for PBL and 11 for SBL. This study revealed new regions related to NSP, but only three associations were related to both branching number (PBN and SBN) and NSP. Two GWAS sites associated with SBL and SBN were stable across contrasting environments and were not related to genes previously reported. The new regions reported in this study can help improving NSP in rice for both direct seeded and transplanted conditions. The integrated approach of high-throughput phenotyping, multi-environment field trials and GWAS has the potential to dissect complex traits, such as NSP, into less complex traits and to match single nucleotide polymorphisms with relevant function under different environments, offering a potential use for molecular breeding.

Highlights: Male fertility decline has been attributed, in part, to increased oxidative stress.Here we will focus on spermatozoa ROS, namely O2 •- , NO and ONOO - and their contribution to protein tyrosine nitration, namely by 3-NT formation.An in depth review will be made on the methods used to detect protein oxidation.Detecting 3-NT in sperm proteins will have a crucial clinical impact, namely on the follow up of anti-oxidant therapies., Abstract: Infertility is a clinical condition that affects around 15% of reproductive-aged couples worldwide. Around half of these cases are due to male factors, the most owing to idiopathic causes. The increase of reactive oxygen species (ROS), which leads to oxidative stress (OS), has been discussed in the last years as a possible cause of male idiopathic infertility. Superoxide anion (O 2 •- ) and nitric oxide (NO) can react with each other contributing to the formation of peroxynitrite (ONOO - ). This molecule can then act on spermatozoa proteins, leading to nitration of protein tyrosines - addition of a nitro (NO 2 ) group - that is then manifested by the formation of 3-nitrotyrosine (3-NT). In turn, 3-NT may be responsible for the alteration or inactivation of the protein function.This review will focus on the description of spermatozoa ROS, namely O 2 •- , NO and ONOO - and in their contribution to protein tyrosine nitration, namely by 3-NT formation. Previous results about the effect of ONOO - and 3-NT in spermatozoa will be presented, as well as, the methods that can be performed to detect the protein oxidation by these species. The impact of measuring, at the clinical level, 3-NT, considered a marker of OS, in spermatozoa will be discussed., Competing Interests: The authors declare no conflicts of interest., (Copyright 2016 PBJ-Associação Porto Biomedical/Porto Biomedical Society.)

Background: Therecent development and availability of different genotype by sequencing (GBS) protocols provided a cost-effective approach to perform high-resolution genomic analysis of entire populations in different species. The central component of all these protocols is the digestion of the initial DNA with known restriction enzymes, to generate sequencing fragments at predictable and reproducible sites. This allows to genotype thousands of genetic markers on populations with hundreds of individuals. Because GBS protocols achieve parallel genotyping through high throughput sequencing (HTS), every GBS protocol must include a bioinformatics pipeline for analysis of HTS data. Our bioinformatics group recently developed the Next Generation Sequencing Eclipse Plugin (NGSEP) for accurate, efficient, and user-friendly analysis of HTS data., Results: Here we present the latest functionalities implemented in NGSEP in the context of the analysis of GBS data. We implemented a one step wizard to perform parallel read alignment, variants identification and genotyping from HTS reads sequenced from entire populations. We added different filters for variants, samples and genotype calls as well as calculation of summary statistics overall and per sample, and diversity statistics per site. NGSEP includes a module to translate genotype calls to some of the most widely used input formats for integration with several tools to perform downstream analyses such as population structure analysis, construction of genetic maps, genetic mapping of complex traits and phenotype prediction for genomic selection. We assessed the accuracy of NGSEP on two highly heterozygous F1 cassava populations and on an inbred common bean population, and we showed that NGSEP provides similar or better accuracy compared to other widely used software packages for variants detection such as GATK, Samtools and Tassel., Conclusions: NGSEP is a powerful, accurate and efficient bioinformatics software tool for analysis of HTS data, and also one of the best bioinformatic packages to facilitate the analysis and to maximize the genomic variability information that can be obtained from GBS experiments for population genomics.

Acoustophoresis refers to the displacement of suspended objects in response to directional forces from sound energy. Given that the suspended objects must be smaller than the incident wavelength of sound and the width of the fluidic channels are typically tens to hundreds of micrometers across, acoustofluidic devices typically use ultrasonic waves generated from a piezoelectric transducer pulsating at high frequencies (in the megahertz range). At characteristic frequencies that depend on the geometry of the device, it is possible to induce the formation of standing waves that can focus particles along desired fluidic streamlines within a bulk flow. Here, we describe a method for the fabrication of acoustophoretic devices from common materials and clean room equipment. We show representative results for the focusing of particles with positive or negative acoustic contrast factors, which move towards the pressure nodes or antinodes of the standing waves, respectively. These devices offer enormous practical utility for precisely positioning large numbers of microscopic entities (e.g., cells) in stationary or flowing fluids for applications ranging from cytometry to assembly.

The precise arrangement of microscopic objects is critical to the development of functional materials and ornately patterned surfaces. Here, we present an acoustics-based method for the rapid arrangement of microscopic particles into organized and programmable architectures, which are periodically spaced within a square assembly chamber. This macroscale device employs two-dimensional bulk acoustic standing waves to propel particles along the base of the chamber toward pressure nodes or antinodes, depending on the acoustic contrast factor of the particle, and is capable of simultaneously creating thousands of size-limited, isotropic and anisotropic assemblies within minutes. We pair experiments with Brownian dynamics simulations to model the migration kinetics and assembly patterns of spherical microparticles. We use these insights to predict and subsequently validate the onset of buckling of the assemblies into three-dimensional clusters by experiments upon increasing the acoustic pressure amplitude and the particle concentration. The simulations are also used to inform our experiments for the assembly of non-spherical particles, which are then recovered via fluid evaporation and directly inspected by electron microscopy. This method for assembly of particles offers several notable advantages over other approaches (e.g., magnetics, electrokinetics and optical tweezing) including simplicity, speed and scalability and can also be used in concert with other such approaches for enhancing the types of assemblies achievable.

Objective: To study the effects of an acute lifestyle change in human semen oxidative stress (OS) by applying seminal parameters and OS markers and to study the feasibility of mid-infrared spectroscopy with Fourier transform infrared spectroscopy (FT-IR) as a complementary tool to evaluate the effects of OS on human sperm samples., Material and Methods: Sperm samples were collected from healthy male students (n=8) who voluntarily submitted themselves to acute lifestyle changes during academic festivities. The samples were obtained before and after the academic festivities and were compared by basic semen analyses and OS markers, namely with thiobarbituric acid reactive species (TBARS) and total thiol (SH) groups by spectrophotometric assays and carbonyl (CO) groups by slot blot. The samples were also submitted for spectroscopic analysis to evaluate the feasibility of FT-IR coupled with multivariate analysis to calibrate OS biomarkers. Statistical analysis was performed applying paired Wilcoxon tests., Results: Acute lifestyle alterations during academic week festivities were associated with a significant decrease in the percentage of normal spermatozoa in the ejaculate (p=0.011) and a decrease in sperm concentration and in semen volume. Regarding OS, acute lifestyle changes promoted a significant increment of TBARS (p=0.018) and an increasing trend in the SH group. With FT-IR and multivariate analysis, it was possible to develop calibration models to the following protein OS biomarkers: SH groups and CO., Conclusions: Acute lifestyle changes during academic festivities have negative effects on sperm quality, in both conventional seminal parameters and OS markers. The evaluation of OS biomarkers and FT-IR could improve andrology diagnosis and therapeutic follow-up.

Early vigour of rice, defined as seedling capacity to accumulate shoot dry weight (SDW) rapidly, is a complex trait. It depends on a genotype propensity to assimilate, store, and/or use non-structural carbohydrates (NSC) for producing large and/or numerous leaves, involving physiological trade-offs in the expression of component traits and, possibly, physiological and genetic linkages. This study explores a plant-model-assisted phenotyping approach to dissect the genetic architecture of rice early vigour, applying the Genome Wide Association Study (GWAS) to morphological and NSC measurements, as well as fitted parameters for the functional-structural plant model, Ecomeristem. Leaf size, number, SDW, and source-leaf NSC concentration were measured on a panel of 123 japonica accessions. The data were used to estimate Ecomeristem genotypic parameters driving organ appearance rate, size, and carbon dynamics. GWAS was performed based on 12 221 single-nucleotide polymorphisms (SNP). Twenty-three associations were detected at P <1×10(-4) and 64 at P <5×10(-4). Associations for NSC and model parameters revealed new regions related to early vigour that had greater significance than morphological traits, providing additional information on the genetic control of early vigour. Plant model parameters were used to characterize physiological and genetic trade-offs among component traits. Twelve associations were related to loci for cloned genes, with nine related to organogenesis, plant height, cell size or cell number. The potential use of these associations as markers for breeding is discussed., (© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Although nearly one fifth of all human cancers have an infectious aetiology, the causes for the majority of cancers remain unexplained. Despite the enormous data output from high-throughput shotgun sequencing, viral DNA in a clinical sample typically constitutes a proportion of host DNA that is too small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low-stringency in-solution hybridization method enables detection of <100 viral copies. Furthermore, distantly related proviral sequences may be enriched by orders of magnitude, enabling discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material.

Aim: This study evaluated the effects of scaling and root planing (SRP) on gingival crevicular fluid (GCF) and serum levels of adipokines in patients with chronic periodontitis (CP) with or without obesity., Methods: Twenty patients with obesity and 20 patients without obesity, all with CP, received SRP. Serum and GCF levels of resistin, adiponectin, leptin, tumour necrosis factor [TNF]-α and interleukin [IL]-6 were evaluated by enzyme-linked immunosorbent assay at baseline, 3, 6 and 12 months post-therapy., Results: SRP reduced the amounts of TNF-α in deep sites and increased the concentration of adiponectin in shallow sites of non-obese patients (p < 0.05). SRP increased the concentrations of TNF-α and leptin in patients with obesity (p < 0.05). GCF levels of TNF-α were higher in patients with obesity than in patients without obesity at all time-points (p < 0.05). There were no changes in serum levels of any adipokines for any group after therapy (p > 0.05). Patients with obesity exhibited higher serum levels of leptin at all time-points and IL-6 at 3 months post-therapy (p < 0.05)., Conclusions: Obesity may modulate systemic and periodontal levels of adipokines in favour of pro-inflammation, independently of periodontal therapy. SRP did not affect the circulating levels of adipokines in patients with or without obesity., (© 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species.

Background and Objectives: The objective of the present study was to evaluate the degree of sedation, intraocular pressure, and hemodynamic changes with premedication with low doses of oral clonidine, 100 microg and 200 microg, in outpatient cataract surgeries., Methods: This is a randomized, double-blind, clinical study undertaken at the Universidade Federal de São Paulo with 60 patients of both genders, physical status ASA 1 and 2, ages 18 to 80 years. Patients were separated into three groups: placebo, clonidine 100 microg, and clonidine 200 microg. Intraocular pressure, heart rate, and blood pressure besides assessment of sedation were measured before and 90 minutes after the administration of clonidine. Sedation levels were classified according to the Ramsay sedation scale., Results: Patients who received placebo and 100 microg of clonidine did not show reduction in heart rate, while a reduction in heart rate was observed in patients who received 200 microg of clonidine, and this difference was statistically significant. Patients who received 200 microg of clonidine also had a reduction in systolic and diastolic blood pressure (p < 0.05). One patient who received 200 microg of clonidine developed severe hypotension, with systolic pressure < 80 mmHg. Patients treated with clonidine had a reduction in intraocular pressure (p < 0.05). Ninety minutes after the oral administration of placebo and 100 microg and 200 microg of clonidine, 25%, 60%, and 80% of the patients respectively were classified as Ramsay 3 or 4., Conclusions: Clonidine 100 microg can be indicated as premedication for fasciectomies, being effective in sedation and reduction of intraocular pressure, without adverse effects on blood pressure and heart rate.