Transition metal-catalyzed iodine(iii)-mediated nitrene transfer reactions: efficient tools for challenging syntheses

The main synthetic applications of catalytic C(sp³)–H amination and alkene aziridination reactions are discussed in the context of natural product synthesis. The examples highlight that these synthetic methods now firmly belong in the organic chemist's toolbox.

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman(®), HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman(®) was found to be the most effective marker of human fecal contamination in this California-based study.

AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data

Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, especially in consanguineous families or isolated populations. Historically, it has been used in conjunction with genotypes from highly polymorphic markers, such as DNA microsatellites or common SNPs. Traditional software performs rather poorly with data from Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS), which are now extensively used in medical genetics. We develop AutoMap, a tool that is both web-based or downloadable, to allow performing homozygosity mapping directly on VCF (Variant Call Format) calls from WES or WGS projects. Following a training step on WES data from 26 consanguineous families and a validation procedure on a matched cohort, our method shows higher overall performances when compared with eight existing tools. Most importantly, when tested on real cases with negative molecular diagnosis from an internal set, AutoMap detects three gene-disease and multiple variant-disease associations that were previously unrecognized, projecting clear benefits for both molecular diagnosis and research activities in medical genetics.

Homozygosity mapping is a useful tool for identifying candidate mutations in recessive conditions, however application to next generation sequencing data has been sub-optimal. Here, the authors present AutoMap, which efficiently identifies runs of homozygosity in whole exome/genome sequencing data.

Mimicry of erythropoietin by a nonpeptide molecule

Erythropoietin (EPO) controls the proliferation and differentiation of erythroid progenitor cells into red blood cells. EPO induces these effects by dimerization of the EPO receptors (EPOR) present on these cells. To discover nonpeptide molecules capable of mimicking the effects of EPO, we identified a small molecule capable of binding to one chain of EPOR and used it to synthesize molecules capable of inducing dimerization of the EPOR. We first identified compound 1 (N-3-[2-(4-biphenyl)-6-chloro-5-methyl]indolyl-acetyl-L-lysine methyl ester) by screening the in-house chemical collection for inhibitors of EPO binding to human EPOR and then prepared compound 5, which contains eight copies of compound 1 held together by a central core. Although both compounds inhibited EPO binding of EPOR, only compound 5 induced dimerization of soluble EPOR. Binding of EPO to its receptor in cells results in activation of many intracellular signaling molecules, including transcription factors like signal transducer and activator of transcription (STAT) proteins, leading to growth and differentiation of these cells. Consistent with its ability to induce dimerization of EPOR in solution, compound 5 exhibited much of the same biological activities as EPO, such as (i) the activation of a STAT-dependent luciferase reporter gene in BAF3 cells expressing human EPOR, (ii) supporting the proliferation of several tumor cell lines expressing the human or mouse EPOR, and (iii) the in vitro differentiation of human progenitor cells into colonies of erythrocytic lineage. These data demonstrate that a nonpeptide molecule is capable of inducing EPOR dimerization and mimicking the biological activities of EPO.

Validation of host-specific Bacteriodales 16S rRNA genes as markers to determine the origin of faecal pollution in Atlantic Rim countries of the European Union

The recent implementation of the Revised Bathing Water Directive in the European Union has highlighted the need for development of effective methods to differentiate between sources of faecal contamination. It had previously been shown that amplification of 16S rRNA genes of host-specific Bacteriodales species using the HF183F and CF128F primers could be used as markers for human and bovine faecal contamination in the United States. This paper determined the sensitivity and specificity of these markers in four Atlantic Rim countries (France, Ireland, Portugal and the United Kingdom) to evaluate their usefulness in determining the origin of faecal contamination. It was shown that the HF183F marker displayed high sensitivity (80-100%) and specificity (91-100%), and is reliable as an indication of human faecal contamination. The CF128F marker displayed 100% sensitivity in all four countries. However, strong regional variations in specificity (41-96%) were observed, highlighting the need for local validation before this marker is employed in source tracking of faecal contamination.

Genetic variability in domesticated Capsicum spp as assessed by morphological and agronomic data in mixed statistical analysis

Capsicum species are very important in Brazil because of economic, cultural and biological factors, and the country is considered to be a diversity center for this genus. Collection and maintenance of the genetic diversity in Capsicum are important to avoid genetic erosion. Besides the identification of species, the characterization and evaluation of accessions maintained in gene banks are of fundamental importance. For this purpose, multivariate methods have become an important tool in the classification of conserved genotypes. The objectives of this study were: i) to identify and characterize accessions of the Capsicum spp collection and draw conclusions about the potential use of certain accessions in different production sectors; ii) to estimate the genetic divergence among accessions using the Ward-MLM procedure, and iii) to evaluate the efficiency of the analysis of continuous and categorical data using the Ward-MLM procedure. Fifty-six Capsicum spp accessions were evaluated based on 25 descriptors, 14 of which were morphological and 11 agronomic. Based on the qualitative descriptors, it was possible to identify all species and, together with the agronomic descriptors, genotypes could be indicated with potential for use in various production sectors. Five was determined as the ideal number of groups by the criteria pseudo-F and pseudo-t2. The Ward-MLM procedure allowed the differentiation of the species C. annuum, C. frutescens, C. baccatum, and C. chinense in separate groups. The Ward-MLM procedure showed some level of efficiency in clustering Capsicum species analyzing morphological and agronomic data simultaneously.

Crimean-Congo hemorrhagic fever virus-infected hepatocytes induce ER-stress and apoptosis crosstalk

Crimean-Congo hemorrhagic fever virus (CCHFV) is a widely distributed tick-borne member of the Nairovirus genus (Bunyaviridae) with a high mortality rate in humans. CCHFV induces a severe disease in infected patients that includes, among other symptoms, massive liver necrosis and failure. The interaction between liver cells and CCHFV is therefore important for understanding the pathogenesis of this disease. Here, we described the in vitro CCHFV-infection and -replication in the hepatocyte cell line, Huh7, and the induced cellular and molecular response modulation. We found that CCHFV was able to infect and replicate to high titres and to induce a cytopathic effect (CPE). We also observed by flow cytometry and real time quantitative RT-PCR evidence of apoptosis, with the participation of the mitochondrial pathway. On the other hand, we showed that the replication of CCHFV in hepatocytes was able to interfere with the death receptor pathway of apoptosis. Furthermore, we found in CCHFV-infected cells the over-expression of PUMA, Noxa and CHOP suggesting the crosstalk between the ER-stress and mitochondrial apoptosis. By ELISA, we observed an increase of IL-8 in response to viral replication; however apoptosis was shown to be independent from IL-8 secretion. When we compared the induced cellular response between CCHFV and DUGV, a mild or non-pathogenic Nairovirus for humans, we found that the most striking difference was the absence of CPE and apoptosis. Despite the XBP1 splicing and PERK gene expression induced by DUGV, no ER-stress and apoptosis crosstalk was observed. Overall, these results suggest that CCHFV is able to induce ER-stress, activate inflammatory mediators and modulate both mitochondrial and death receptor pathways of apoptosis in hepatocyte cells, which may, in part, explain the role of the liver in the pathogenesis of CCHFV.

Chromosome imbalances in thyroid follicular neoplasms: a comparison between follicular adenomas and carcinomas

The underlying genetic events associated with follicular thyroid tumorigenesis are still ill defined. In this study, we performed a screening for chromosome imbalances by comparative genomic hybridization (CGH) in a group of 12 follicular adenomas (FAs) and 20 follicular carcinomas (FTCs) previously characterized by conventional cytogenetics and flow cytometry analysis. In general, a great similarity was observed between the CGH profiles of the FAs and FTCs. In both benign and malignant tumors, a combination of gains affecting 5, 7, 12, 17, 19, and 20 was observed. Chromosome 7 was the most frequently affected chromosome, with three regions of consensus gains: 7p11-12, 7q11.3-q21, and 7q31. Recurrent gains of chromosomes 5 and 12 involved 5p11, 5p15, 5q13-q22, 5q21-q23, 12p11, and 12q11-q12. DNA sequence losses were also observed in both tumor groups. Chromosomal arms deleted in at least five of the neoplasms were (in order of frequency): in adenomas, 15q, 2p/2q, 3q, 6p/6q, 11q, and 22q; and in FTCs, 3p, 2p, 8q, 1p, 2q, 3q, 6q, 8p, 9p, 11q, 13q, 6p, and 18q. The statistical evaluation of the CGH data demonstrated that 15q loss was significantly associated with FA. Two regions of minimal common loss were defined by CGH at 15: 15q11-q21 and 15q26-qter. The identification of these regions provides a basis for further molecular studies.

RiboCas: A Universal CRISPR-Based Editing Tool for Clostridium

Members of the genus Clostridium represent a diverse assemblage of species exhibiting both medical and industrial importance. Deriving both a greater understanding of their biology, while at the same time enhancing their exploitable properties, requires effective genome editing tools. Here, we demonstrate the first implementation in the genus of theophylline-dependent, synthetic riboswitches exhibiting a full set of dynamic ranges, also suitable for applications where tight control of gene expression is required. Their utility was highlighted by generating a novel riboswitch-based editing tool-RiboCas-that overcomes the main obstacles associated with CRISPR/Cas9 systems, including low transformation efficiencies and excessive Cas9 toxicity. The universal nature of the tool was established by obtaining chromosomal modifications in C. pasteurianum, C. difficile, and C. sporogenes, as well as by carrying out the first reported example of CRISPR-targeted gene disruption in C. botulinum. The high efficiency (100% mutant generation) and ease of application of RiboCas make it suitable for use in a diverse range of microorganisms.

Impact of adherence to antiretroviral therapy in HIV-1-infected patients at a university public service in Brazil

The objective of this study was to assess if a simple evaluation, adherence to antiretroviral therapy, would correlate to clinical and laboratory outcomes. We followed an open cohort of patients from a public teaching hospital AIDS outpatient clinic. Patients were categorized according to adherence as: regular (Reg), optimal, all doses all days, tolerating only irregular timing (+/- 2 hours) of intake; quasi-regular (qReg), those missing up to four doses or 1 full day during a month; irregular (Irreg), all other irregular regimens, and ignored (Ign), those without information. The results from a simple questionnaire were compared to CD4+ cell counts and human immunodeficiency virus type 1 (HIV-1) RNA plasma viremia. One hundred eighty-two HIV-1-infected patients (126 males, 69%; 56 females, 31%) were analyzed. Information on adherence was available for 168 (90%). Reg adherence was reported by 75 (41%) patients, qReg adherence by 35 (19%), and Irreg by 53 (29%) of patients. The main reasons for nonadherence were forgetfulness, intolerance, use of alcohol, and misunderstanding of prescription. A significant increase of CD4+ T-cell counts and absolute gain were only observed among Reg and qReg users (p < 0.001). The median viral RNA load log10 decreases were -1.68, -1.45, -0.9 log, respectively, for Reg, qReg, and Irreg patients (p = 0.043, Kruskal-Wallis). Development of and death from AIDS occurred almost exclusively among those with Ign or Irreg adherence. Previous use of antiretroviral therapy may have had an impact in treatment response. Individuals who were treatment-naive were more likely to be Reg users (41%). Although more refined methods to assess adherence should be implemented when available, the inability to do so should not prevent simple, albeit subjective measurements that also correlate with favorable outcome. Mechanisms to improve adherence should be considered an integral part of antiretroviral therapy.

Differential activation profiles of Crimean-Congo hemorrhagic fever virus- and Dugbe virus-infected antigen-presenting cells

Crimean-Congo hemorrhagic fever virus (CCHFV) is a highly pathogenic, tick-borne member of the family Bunyaviridae and the genus Nairovirus. To better elucidate the pathogenesis of CCHFV, we analysed the host innate immune response induced in antigen-presenting cells (APCs) infected in vitro by CCHFV. Monocyte-derived dendritic cells (DCs) and macrophages (MPs) were both shown to be permissive for CCHFV and to replicate the virus, as monitored by genomic and antigenomic strand quantification. Virus replication was, however, controlled, corroborating an efficient alpha interferon-induced response. The upregulation of CD-83 and CD-86 indicated that CCHFV induced a partial maturation of DCs, which were also shown to activate the secretion of interleukin (IL)-6 and IL-8, but no tumour necrosis factor alpha (TNF-alpha). On the other hand, in MPs, CCHFV infection elicited a high IL-6 and TNF-alpha response and a moderate chemokine response. Nevertheless, when we compared these APC responses with those seen after infection with Dugbe virus (DUGV), a mildly pathogenic virus genetically close to CCHFV, we found that, in spite of some similarities, DUGV induced a higher cytokine/chemokine response in MPs. These results suggest that CCHFV is able to inhibit the activation of inflammatory mediators selectively in infection in vitro and that these differences could be relevant in pathogenesis.

Comparison of multivariate statistical algorithms to cluster tomato heirloom accessions

Use of multivariate statistical algorithms is considered an important strategy to quantify genetic similarity. Local varieties and traditional (heirloom) seeds of genotypes are key sources of genetic variation. The Universidade Estadual do Norte Fluminense (UENF), Rio de Janeiro, Brazil, has a tomato gene bank with accessions that have been maintained for more than 40 years. We compared various algorithms to estimate genetic distances and quantify the genetic divergence of 40 tomato accessions of this collection, based on separate and joint analyses of discrete and continuous variables. Differences in continuous variables and discrete and joint analyses were calculated based on the Mahalanobis, Cole Rodgers and Gower distances. Although opinions differ regarding the validity of joint analysis of discrete and continuous data, we found that analyzing a larger number of variables together is viable and can help in the discrimination of accessions; the information that is generated is relevant and promising for both, the accessions conservation and the use of genetic resources in breeding programs.

Routine screening of harmful microorganisms in beach sands: implications to public health

Beaches worldwide provide recreational opportunities to hundreds of millions of people and serve as important components of coastal economies. Beach water is often monitored for microbiological quality to detect the presence of indicators of human sewage contamination so as to prevent public health outbreaks associated with water contact. However, growing evidence suggests that beach sand can harbor microbes harmful to human health, often in concentrations greater than the beach water. Currently, there are no standards for monitoring, sampling, analyzing, or managing beach sand quality. In addition to indicator microbes, growing evidence has identified pathogenic bacteria, viruses, and fungi in a variety of beach sands worldwide. The public health threat associated with these populations through direct and indirect contact is unknown because so little research has been conducted relating to health outcomes associated with sand quality. In this manuscript, we present the consensus findings of a workshop of experts convened in Lisbon, Portugal to discuss the current state of knowledge on beach sand microbiological quality and to develop suggestions for standardizing the evaluation of sand at coastal beaches. The expert group at the "Microareias 2012" workshop recommends that 1) beach sand should be screened for a variety of pathogens harmful to human health, and sand monitoring should then be initiated alongside regular water monitoring; 2) sampling and analysis protocols should be standardized to allow proper comparisons among beach locations; and 3) further studies are needed to estimate human health risk with exposure to contaminated beach sand. Much of the manuscript is focused on research specific to Portugal, but similar results have been found elsewhere, and the findings have worldwide implications.

Non-vitamin K antagonist oral anticoagulants in elderly patients with atrial fibrillation: A systematic review with meta-analysis and trial sequential analysis

BACKGROUND

Elderly population is known to be associated with polymedication, comorbidities and altered drug pharmacokinetics. However, the most adequate oral anticoagulant, attending to its relative efficacy and safety, remains unclear.

METHODS

We searched for phase III randomized controlled trials (MEDLINE, Cochrane Library, SciELO collection and Web of Science) comparing novel non-vitamin K antagonist oral anticoagulants (NOACs) with Vitamin K antagonists (VKA) in the elderly population (≥75 years-old) in atrial fibrillation (AF). Risk ratios (RR) were calculated using a random effects model. Trial sequential analysis (TSA) was performed in statistically significant results to evaluate whether cumulative sample size was powered.

RESULTS

Four trials rendered data about elderly (≥75 years-old) and younger patients (<75 years-old) with AF. NOACs demonstrated a 30% significant risk reduction (RR 0.70, 95% CI: 0.61 to 0.80) in elderly patients compared to VKA, without heterogeneity across studies (I² = 0%). The TSA showed that cumulative evidence of this subgroup exceeded the minimum information size required for the risk reduction. In younger patients, VKA and NOACs shared a similar risk of stroke and systemic embolism (RR 0.97, 95% CI: 0.79 to 1.18). Regarding major bleeding risk in the elderly, the overall comparative risk of NOACs was not different from VKA (RR 0.91, 95% CI: 0.72 to 1.16; I² = 86%).

CONCLUSIONS

NOACs reduce significantly the risk of stroke and systemic embolism in elderly patients without increasing major bleeding events. The dimension of stroke risk reduction was significantly higher in the elderly than in younger adults.

Immunoprofile of α-Gal- and B-antigen-specific responses differentiates red meat-allergic patients from healthy individuals

BACKGROUND

The galactose-α-1,3-galactose (α-Gal) epitope is involved in red meat allergy. As α-Gal is structurally similar to the blood group B-antigen, we explored the relationship between the immune responses to α-Gal- and the B-antigen in red meat-allergic patients compared to healthy A/O or B blood donors.

METHODS

Sera from 51 red meat-allergic patients IgE-positive to α-Gal and 102 healthy blood donors (51 blood group A/O; 51 blood group B) were included. α-Gal- and B-antigen-specific IgE (ImmunoCAP) and IgG/IgG_1-4 (ELISA) responses were determined. Basophil activation tests were performed.

RESULTS

Fifteen healthy donors were IgE positive to α-Gal, of which 3 had blood group B. The allergic patients had significantly higher α-Gal IgE levels compared to the healthy donors. The majority of the allergic patients, but none of the healthy donors, had IgE against the B-antigen. Inhibition studies revealed cross-reactivity between α-Gal and the B-antigen. The biological activity of the B-antigen was confirmed by basophil activation tests. Anti-α-Gal IgG₁ and IgG₄ levels were significantly higher in the patients compared to the healthy donors. Moreover, the IgG response to the B-antigen was comparable between the allergic patients and healthy A/O donors.

CONCLUSION

Red meat-allergic patients showed significantly higher α-Gal IgE, IgG₁ , and IgG₄ levels, reflecting a Th2 response, compared to healthy blood donors. Blood group B donors had significantly reduced antibody responses to α-Gal, due to similarities with the B-antigen, resulting in a lower risk of sensitization to α-Gal and development of red meat allergy.

Subaortic fibrous ridge and ventricular septal defect: role of septal malalignment

The purpose of this study was to test the hypothesis that the presence of a subaortic ridge associated with a ventricular septal defect (VSD) is related to a malaligned ventricular septum caused by anterior or posterior deviation of the infundibular septum with or without obstructive lesions of the aortic arch. Thirty-two of 295 patients in whom a diagnosis of VSD was made by two-dimensional echocardiography and who were studied from June 1983 to April 1985 presented with a subaortic shelf. Every patient (p less than .00001) had a malalignment type of defect; the defect was produced by anterior deviation of the outlet septum (without compromise of the right ventricular outflow tract) in 28 and by posterior deviation of the infundibular septum in four. The prevalence of a subaortic shelf in the malalignment VSD group was 82% (32/39). Among the 28 patients with a subaortic ridge and anterior deviation of the outlet septum only three had aortic coarctation, but all four patients with subaortic stenosis and posterior infundibular malalignment had obstructive lesions of the aortic arch--coarctation in three and interruption of the aortic arch in one (p less than .001). We conclude that a malalignment type of VSD may be a consistent feature in patients with VSD and associated discrete subaortic stenosis. We also noted a high prevalence of subaortic ridge in the presence of a malalignment VSD and therefore speculate that there may be a common morphogenesis for malalignment VSD, subaortic shelf, and obstructive lesions of the aortic arch.

Pathogenic fungi: an unacknowledged risk at coastal resorts? New insights on microbiological sand quality in Portugal

Whilst the potential impact on beach users from microorganisms in water has received considerable attention, there has been relatively little investigation into microbial contaminants in sand. Thirty three beaches across Portugal were analyzed during a five year period (2006-2010) to determine the presence of yeasts, pathogenic fungi, dermatophytes, total coliforms, Escherichia coli and intestinal enterococci in sand. Our results showed that 60.4% of the samples were positive for fungi and that 25.2% were positive for the bacterial parameters. The most frequent fungal species found were Candida sp. and Aspergillus sp., whereas intestinal enterococci were the most frequently isolated bacteria. Positive associations were detected among analyzed parameters and country-regions but none among those parameters and sampling period. Regarding threshold values, we propose 15 cfu/g for yeasts, 17 cfu/g for potential pathogenic fungi, 8 cfu/g for dermatophytes. Twenty-five cfu/g for E. coli, and 10 [corrected] cfu/g for intestinal enterococci.

Randomized comparison between intravaginal misoprostol and dinoprostone for cervical ripening and induction of labor

OBJECTIVE

We sought to evaluate the efficacy and safety of intravaginal misoprostol and dinoprostone for labor induction.

STUDY DESIGN

One hundred eighty-nine women with singleton term pregnancies and unfavorable cervices were randomly assigned to receive intravaginal misoprostol or dinoprostone. The outcome variables were change in Bishop score, time from application to active phase of labor and delivery, fetal and maternal morbidity, and the incidence of cesarean deliveries.

RESULTS

The interval from application of the initial dose to the beginning of the active phase of labor was 9.8 +/- 5.8 and 14.2 +/- 10.2 hours (P <.01), and the interval from initial dose to delivery was 15.3 +/- 9.8 and 19.1 +/- 13.2 hours (P =.027) for the misoprostol and dinoprostone groups, respectively. There were no significant differences in Bishop score change, cesarean delivery rate, and the incidence of tachysystole, hypersystole, and hyperstimulation. No maternal and neonatal adverse effects were noted.

CONCLUSION

Intravaginal misoprostol is more effective than intravaginal dinoprostone for labor induction in low-risk patients at term with unfavorable cervices.

Action of a pentacyclic triterpenoid, maslinic acid, against Toxoplasma gondii

The action of maslinic acid (2alpha,3beta-dihydroxyolean-12-en-28-oic acid) (1), a pentacyclic derivative present in the pressed fruits of the olive (Olea europaea), has been studied against the tachyzoites of Toxoplasma gondii. The capability of tachyzoites to infect Vero cells treated with 1 was affected. The LD(50) values were 58.2 muM for the isolated tachyzoites and 236 muM for the noninfected Vero cells. Zymograms of the T. gondii proteases incubated with 1 showed a dosage-dependent inhibition of some of the proteases. The parasites treated with 1 showed gliding motility and ultrastructural alterations. The present findings suggest that protease activity of the parasite required for cell invasion is the action target for maslinic acid (1).