Mimicking Behçet's disease: GM-CSF gain of function mutation in a family suffering from a Behçet's disease-like disorder marked by extreme pathergy

Behçet's disease (BD) is an inflammatory disease mainly affecting men along the ancient Silk Route. In the present study we describe a Dutch family suffering from BD-like disease with extreme pathergic responses, but without systemic inflammation. Genetic assessment revealed a combination of the human leukocyte antigen (HLA)-B*51 risk-allele together with a rare heterozygous variant in the CSF2 gene (c.130A>C, p.N44H) encoding for granulocyte-macrophage colony-stimulating factor (GM-CSF) found by whole exome sequencing. We utilized an over-expression vector system in a human hepatocyte cell line to produce the aberrant variant of GM-CSF. Biological activity of the protein was measured by signal transducer and activator of transcription 5 (STAT-5) phosphorylation, a downstream molecule of the GM-CSF receptor, in wild-type peripheral mononuclear cells (PBMCs) using flow cytometry. Increased STAT-5 phosphorylation was observed in response to mutated GM-CSF when compared to the wild-type or recombinant protein. CSF2 p.N44H results in disruption of one of the protein's two N-glycosylation sites. Enzymatically deglycosylated wild-type GM-CSF also enhanced STAT-5 phosphorylation. The patient responded well to anti-tumor necrosis factor (TNF)-α treatment, which may be linked to the capacity of TNF-α to induce GM-CSF in phorbol 12-myristate 13-acetate (PMA)-treated PBMCs, while GM-CSF itself only induced dose-dependent interleukin (IL)-1Ra production. The identified CSF2 pathway could provide novel insights into the pathergic response of BD-like disease and offer new opportunities for personalized treatment.

Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.

Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.

Genetic identity in genebanks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection

Breeders rely on genetic integrity of material from genebanks; however, admixture, mislabeling, and errors in original data can occur and be detrimental. Two hundred and fifty accessions, representing paired samples consisting of original mother plants and their in vitro counterparts from the cultivated potato collection at the International Potato Center (CIP) were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity of the accessions and evaluate genetic diversity of the potato collection. Diploid, triploid, and tetraploid accessions were included, representing seven cultivated potato taxa (based on Hawkes, 1990). Fingerprints between voucher mother plants maintained in the field and in vitro clones of the same accession were used to evaluate identity, relatedness, and ancestry using hierarchal clustering and model-based Bayesian admixture analyses. Generally, in vitro and field clones of the same accession grouped together; however, 11 (4.4%) accessions were mismatches genetically, and in some cases the SNP data revealed the identity of the mixed accession. SNP genotypes were used to assess genetic diversity and to evaluate inter- and intraspecific relationships along with determining population structure and hybrid origins. Phylogenetic analyses suggest that the triploids included in this study are genetically similar. Further, some genetic redundancies among individual accessions were also identified along with some putative misclassified accessions. Accessions generally clustered together based on taxonomic classification and ploidy level with some deviations. STRUCTURE analysis identified six populations with significant gene flow among the populations, as well as revealed hybrid taxa and accessions. Overall, the Infinium 12K V2 Potato Array proved useful in confirming identity and highlighting the diversity in this subset of the CIP collection, providing new insights into the accessions evaluated. This study provides a model for genetic identity of plant genetic resources collections as mistakes in conservation of these collections and in genebanks is a reality. For breeders and other users of these collections, confirmed identity is critical, as well as for quality management programs and to provide insights into the accessions evaluated.

NF-κB pathway controls mitochondrial dynamics

The Optic atrophy 1 protein (OPA1) is a key element in the dynamics and morphology of mitochondria. We demonstrated that the absence of IκB kinase-α, which is a key element of the nonclassical NF-κB pathway, has an impact on the mitochondrial network morphology and OPA1 expression. In contrast, the absence of NF-κB essential modulator (NEMO) or IκB kinase-β, both of which are essential for the canonical NF-κB pathway, has no impact on mitochondrial dynamics. Whereas Parkin has been reported to positively regulate the expression of OPA1 through NEMO, herein we found that PARK2 overexpression did not modify the expression of OPA1. PARK2 expression reduced the levels of Bax, and it prevented stress-induced cell death only in Bak-deficient mouse embryonic fibroblast cells. Collectively, our results point out a role of the nonclassical NF-κB pathway in the regulation of mitochondrial dynamics and OPA1 expression.

Complete genome sequences of new divergent potato virus X isolates and discrimination between strains in a mixed infection using small RNAs sequencing approach

Potato virus X (PVX; genus Potexvirus, family Alphaflexiviridae, order Tymovirales) is one of the most widespread and intensively studied viruses of potato. However, little is known about its diversity in its likely center of radiation, the Andean region of South America. To fill this gap, the strategy of Illumina deep sequencing of small RNAs was used to obtain complete or near complete genome sequence of PVX from 5 symptomatically infected greenhouse and 3 field samples (Solanum tuberosum) from Peru. PVX sequences determined in this study were assigned into three different phylogenetic groups of isolates. Notably, a complete genome sequence of a representative of a new PVX phylogenetic lineage was obtained, which shows a high level of sequence dissimilarity to other completely sequenced isolates (∼17%). The new PVX genotype was detected in greenhouse and field samples. One of the field samples was infected with the mixture of two PVX strains, which were efficiently discriminated using small RNA sequencing approach. The study confirms the utility of small RNAs deep sequencing for successful viral strain differentiation and discovery of new viral strains and indicates a high diversity of PVX in the Andean region of South America, a pattern which may be expected also for other potato pathogens.

Modulation of mammalian apoptotic pathways by intracellular protozoan parasites

During intracellular parasitic infections, pathogens and host cells take part in a complex web of events that are crucial for the outcome of the infection. Modulation of host cell apoptosis by pathogens attracted the attention of scientists during the last decade. Apoptosis is an efficient mechanism used by the host to control infection and limit pathogen multiplication and dissemination. In order to ensure completion of their complex life cycles and to guarantee transmission between different hosts, intracellular parasites have developed mechanisms to block apoptosis and sustain the viability of their host cells. Here, we review how some of the most prominent intracellular protozoan parasites modulate the main mammalian apoptotic pathways by emphasizing the advances from the last decade, which have begun to dissect this dynamic and complex interaction.

The Leishmania nicotinamidase is essential for NAD+ production and parasite proliferation

NAD+ is a central cofactor that plays important roles in cellular metabolism and energy production in all living cells. Genomics-based reconstruction of NAD+ metabolism revealed that Leishmania protozoan parasites are NAD+ auxotrophs. Consequently, these parasites require assimilating NAD+ precursors (nicotinamide, nicotinic acid, nicotinamide riboside) from their host environment to synthesize NAD+ by a salvage pathway. Nicotinamidase is a key enzyme of this salvage pathway that catalyses conversion of nicotinamide (NAm) to nicotinic acid (Na), and that is absent in higher eukaryotes. We present here the biochemical and functional characterizations of the Leishmania infantum nicotinamidase (LiPNC1). Generation of Lipnc1 null mutants leads to a decrease in NAD+ content, associated with a metabolic shutdown-like phenotype with an extensive lag phase of growth. Both phenotypes could be rescued by an add-back construct or by addition of exogenous Na. In addition, Lipnc1 null mutants were unable to establish a sustained infection in a murine experimental model. Altogether, these results illustrate that NAD+ homeostasis is a fundamental component of Leishmania biology and virulence, and that NAm constitutes its main NAD+ source in the mammalian host. The crystal structure of LiPNC1 we solved allows now the design of rational inhibitors against this new promising therapeutic target.

First Report of Potato yellowing virus (Genus Ilarvirus) in Solanum phureja from Ecuador

A bacilliform virus, named Potato yellowing virus (PYV), causing chlorosis of leaves was reported in 1992 in potato (Solanum tuberosum) fields in Peru (1) and symptomless wild potatoes (S. fernandezianum) in Chile (4). PYV is reported as an alfamo-like virus (1) (family Bromoviridae) but no sequence information is available for this virus, making its taxonomic position inside the Bromoviridae uncertain (currently this family is organized into five genera: Alfamovirus, Bromovirus, Cucumovirus, Ilarvirus, and Oleavirus). Herein we report the presence of PYV in native potatoes (Solanum phureja) collected from Ecuador where the crop constitutes an important source of income in rural communities. Forty accessions of S. phureja collected in Ecuador in June 1986 and maintained in vitro at the International Potato Center (CIP) germplasm bank were analyzed by double-antibody sandwich (DAS)-ELISA with antiserum raised against a Peruvian isolate of PYV (1). PYV was detected in six accessions (15% of the material) corresponding to cultivars Chaucha Tomate and Chaucha Blanca (from the province of Cañar), Chaucha Negra Ojona and Chaucha Amarilla (Loja Province), and Cuica and Chaucha (Azuay Province). Mechanical inoculation of the indicator plant Physalis floridiana with leaf extracts of these six plants, a PYV isolate from Peru (1) (positive control), and an additional four plants testing negative for PYV (negative controls) induced symptoms of mosaic and leaf deformation only with the six clones from Ecuador and the PYV isolate from Peru. To further confirm the presence of the virus, we used universal PCR primers designed for the Bromoviridae (Ilar1F5: 5'-GCNGGWTGYGGDAARWCNAC-3' and Ilar1R7: 5'-AMDGGWAYYTGYTYNGTRTCACC-3') that target the helicase motif (RNA1) (3). Total RNA was extracted from 200 mg of leaf material (from potato and mechanically inoculated P. floridiana) using Trizol (Invitrogen, Carlsbad, CA) following the manufacturer's instructions and cDNA was synthesized using random hexamer primers. We obtained a reverse transcription-PCR amplified band only from samples that were DAS-ELISA positive to PYV. To identify the virus at the genus level, we cloned the PCR fragments (265 nucleotides) from four of the samples from Ecuador and the Peruvian isolate into plasmid vectors (pGEM-T Easy Vector cloning system; Promega, Madison, WI) for Sanger sequencing (Macrogen, Seoul, Korea). Phylogenetic analysis grouped PYV sequences with those of the genus Ilarvirus. Among the ilarviruses, Fragaria chiloensis latent virus (2) was the closest relative of PYV, with which it shares 77% nucleotide and 85% amino acid sequence identity. PYV isolates from Ecuador split into two different variants (91% identity) that shared 93% nucleotide and 99% amino acid sequence identity with the Peruvian isolate. Collectively, the data suggest that PYV is a distinct ilarvirus and that it is more widely spread among South American potatoes than previously suggested. The GenBank Accession Numbers for the sequences described are: HQ141053 (Loja1), HQ141054 (Azuay), HQ141055 (Cañar), and HQ141056 (Loja2) for the isolates from Ecuador and HQ141057 (PYV-Cañete) for the isolate from Peru. References: (1) S. Fuentes and U. Jayasinghe. Fitopatología 28:22, 1993. (2) I. E. Tzanetakis and R. R. Martin. Virus Res. 112:32, 2005. (3) M. Untiveros et al. J. Virol. Methods 165:97, 2010. (4) J. P. T. Valkonen et al. Potato Res. 35:411, 1992.

FDG PET for the routine follow-up in NHL: First prospective evaluation

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Background: We have shown that FDG PET is able to detect preclinical relapses in patients with Hodgkin’s disease but the high rate of false-positivity (55%) was a problem (Jerusalem et al, Ann Oncol, 2003; 14 : 123–130). The aim of this study was to determine the accuracy of PET during follow-up after treatment in non-Hodgkin’s lymphoma (NHL). Methods: Patients were eligible if they had a positive baseline FDG PET and a negative end of treatment work-up including a negative PET study. They underwent FDG PET every 4–6 months until 3 years after diagnosis. Forty-five aggressive NHL (diffuse large B-cell lymphoma : 34, other : 11) and eighteen low grade NHL (follicular lymphoma : 16, other : 2) were recruited prospectively between 5/94 and 12/01. Results: A total of 197 FDG PET studies were realized. Six patients relapsed (aggressive NHL : 4, low grade NHL : 2) and 3 patients died (aggressive NHL : 2, pancreatic cancer : 1) during the time interval of the study protocol. Four asymptomatic relapses (aggressive NHL : 2, low grade NHL : 2) and one symptomatic relapse (aggressive NHL) was detected by FDG PET. Disease recurrence became symptomatic or clinically detectable a week, 3 months (both aggressive NHL), 12 and 17 months (both low grade NHL) after the first positive PET study. The latter had 4 positive FDG PET studies before biopsy-proven relapse. The time interval between the only false-negative PET and clinical relapse was 5 months in a patient with aggressive NHL. We observed for the whole study population a sensitivity of 89% (8/9), a specificity of 93% (174/188), a positive predictive value of 36% (8/22), a negative predictive value (NPV) of 99% (174/175) and an accuracy of 92% (182/197). In low grade NHL PET had a sensitivity of 100% (5/5), a specificity of 93% (50/54), a PPV of 56% (5/9), a NPV of 100% (50/50) and an accuracy of 93% (55/59). In aggressive NHL, PET had a sensitivity of 75% (3/4), a specificity of 93% (124/134), a PPV 23% (3/13), a NPV of 99% (124/125) and an accuracy of 92% (127/138). Conclusions: In aggressive NHL, routine follow-up by FDG PET is not very useful and we stopped it now in unselected aggressive NHL. In contrast, FDG PET can detect a relapse several months before the development of clinical symptoms in low grade NHL suggesting further evaluation of the role of PET in the routine follow-up of these patients.

No significant financial relationships to disclose.

In vitro antileishmanial activity of nicotinamide

Our study represents the first report demonstrating the antileishmanial activity of nicotinamide (NAm), a form of vitamin B(3). A 5 mM concentration of NAm significantly inhibited the intracellular growth of Leishmania amastigotes and the NAD-dependent deacetylase activity carried by parasites overexpressing Leishmania major SIR2 (LmSIR2). However, the transgenic parasites were as susceptible as the wild-type parasites to NAm-induced cell growth arrest. Therefore, we conclude that NAm inhibits leishmanial growth and that overexpression of LmSIR2 does not overcome this inhibition. The mechanism of the inhibition is not defined but may include other in vivo targets. NAm may thus represent a new antileishmanial agent which could potentially be used in combination with other drugs during therapy.

Tumeur mélanocytaire méningée primitive de grade intermédiaire : confrontation radio-pathologique

A case of primary meningeal intermediate grade melanocytic neoplasm involving the right C2 nerve root is presented. MRI findings may suggest this rare entity, especially when an extra-axial lesion is located in the posterior fossa or cervical spinal canal and demonstrates shortening of both T1 and T2. Eventually, definitive diagnosis relies on histology which demonstrates spindle-shaped melanocytic cells that are Fontana stained and positive for HMB:45 antigen. Cellularity, pleomorphism, mitotic rate, proliferation index and invasiveness are useful criteria to distinguish among the spectrum of primary melanocytic tumors of the central nervous system ranging from melanocytoma to malignant melanoma.

Comparison of energy-restricted very low-carbohydrate and low-fat diets on weight loss and body composition in overweight men and women

OBJECTIVE: To compare the effects of isocaloric, energy-restricted very low-carbohydrate ketogenic (VLCK) and low-fat (LF) diets on weight loss, body composition, trunk fat mass, and resting energy expenditure (REE) in overweight/obese men and women. DESIGN: Randomized, balanced, two diet period clinical intervention study. Subjects were prescribed two energy-restricted (-500 kcal/day) diets: a VLCK diet with a goal to decrease carbohydrate levels below 10% of energy and induce ketosis and a LF diet with a goal similar to national recommendations (%carbohydrate:fat:protein = ~60:25:15%). SUBJECTS: 15 healthy, overweight/obese men (mean +/- s.e.m.: age 33.2 +/- 2.9 y, body mass 109.1 +/- 4.6 kg, body mass index 34.1 +/- 1.1 kg/m2) and 13 premenopausal women (age 34.0 +/- 2.4 y, body mass 76.3 +/- 3.6 kg, body mass index 29.6 +/- 1.1 kg/m2). MEASUREMENTS: Weight loss, body composition, trunk fat (by dual-energy X-ray absorptiometry), and resting energy expenditure (REE) were determined at baseline and after each diet intervention. Data were analyzed for between group differences considering the first diet phase only and within group differences considering the response to both diets within each person. RESULTS: Actual nutrient intakes from food records during the VLCK (%carbohydrate:fat:protein = ~9:63:28%) and the LF (~58:22:20%) were significantly different. Dietary energy was restricted, but was slightly higher during the VLCK (1855 kcal/day) compared to the LF (1562 kcal/day) diet for men. Both between and within group comparisons revealed a distinct advantage of a VLCK over a LF diet for weight loss, total fat loss, and trunk fat loss for men (despite significantly greater energy intake). The majority of women also responded more favorably to the VLCK diet, especially in terms of trunk fat loss. The greater reduction in trunk fat was not merely due to the greater total fat loss, because the ratio of trunk fat/total fat was also significantly reduced during the VLCK diet in men and women. Absolute REE (kcal/day) was decreased with both diets as expected, but REE expressed relative to body mass (kcal/kg), was better maintained on the VLCK diet for men only. Individual responses clearly show the majority of men and women experience greater weight and fat loss on a VLCK than a LF diet. CONCLUSION: This study shows a clear benefit of a VLCK over LF diet for short-term body weight and fat loss, especially in men. A preferential loss of fat in the trunk region with a VLCK diet is novel and potentially clinically significant but requires further validation. These data provide additional support for the concept of metabolic advantage with diets representing extremes in macronutrient distribution.