Sequencing of the Dutch Elm Disease Fungus Genome Using the Roche/454 GS-FLX Titanium System in a Comparison of Multiple Genomics Core Facilities

As part of the DNA Sequencing Research Group of the Association of Biomolecular Resource Facilities, we have tested the reproducibility of the Roche/454 GS-FLX Titanium System at five core facilities. Experience with the Roche/454 system ranged from <10 to >340 sequencing runs performed. All participating sites were supplied with an aliquot of a common DNA preparation and were requested to conduct sequencing at a common loading condition. The evaluation of sequencing yield and accuracy metrics was assessed at a single site. The study was conducted using a laboratory strain of the Dutch elm disease fungus Ophiostoma novo-ulmi strain H327, an ascomycete, vegetatively haploid fungus with an estimated genome size of 30–50 Mb. We show that the Titanium System is reproducible, with some variation detected in loading conditions, sequencing yield, and homopolymer length accuracy. We demonstrate that reads shorter than the theoretical minimum length are of lower overall quality and not simply truncated reads. The O. novo-ulmi H327 genome assembly is 31.8 Mb and is comprised of eight chromosome-length linear scaffolds, a circular mitochondrial conti of 66.4 kb, and a putative 4.2-kb linear plasmid. We estimate that the nuclear genome encodes 8613 protein coding genes, and the mitochondrion encodes 15 genes and 26 tRNAs.     

Cisgenics as emerging bio-objects: bio-objectification and bio-identification in agrobiotech innovation

Cisgenesis is a genetic modification of a recipient organism with genetic material from a crossable organism. Trying to free cisgenics from the regulatory guidelines of genetically modified organisms (GMOs), some scientists have suggested to classify the genetically modified products by the origin of transferred genes. Aiming at exploring how scientists frame cisgenics in relation to current legal frameworks, we have sent an extensive survey to the totality of researchers working on cisgenics. Trying to provide cisgenics with a new, uncontroversial identity, the respondents present cisgenics as a method of obtaining “natural,” environmentally friendly and economically sustainable crops. However, such strategy is challenged by GMO corporations opposing a segmentation of the sector, and by the opponents of GMOs, who fear that deregulation on cisgenics leads to the deregulation of GMOs. Drawing from the concepts of bio-objectification and bio-identification, we show how the status of this bio-object is likely to remain contested and contestable.     

The Cannabinoid Receptor Type 2 as Mediator of Mesenchymal Stromal Cell Immunosuppressive Properties

Mesenchymal stromal cells are non-hematopoietic, multipotent progenitor cells producing cytokines, chemokines, and extracellular matrix proteins that support hematopoietic stem cell survival and engraftment, influence immune effector cell development, maturation, and function, and inhibit alloreactive T-cell responses. The immunosuppressive properties of human mesenchymal stromal cells have attracted much attention from immunologists, stem cell biologists and clinicians.Recently, the presence of the endocannabinoid system in hematopoietic and neural stem cells has been demonstrated. Endocannabinoids, mainly acting through the cannabinoid receptor subtype 2, are able to modulate cytokine release and to act as immunosuppressant when added to activated T lymphocytes.In the present study, we have investigated, through a multidisciplinary approach, the involvement of the endocannabinoids in migration, viability and cytokine release of human mesenchymal stromal cells.We show, for the first time, that cultures of human mesenchymal stromal cells express all of the components of the endocannabinoid system, suggesting a potential role for the cannabinoid CB2 receptor as a mediator of anti-inflammatory properties of human mesenchymal stromal cells, as well as of their survival pathways and their capability to home and migrate towards endocannabinoid sources.     

Extramotor Damage Is Associated with Cognition in Primary Lateral Sclerosis Patients

Objectives

This is a cross-sectional study aimed at investigating cognitive performances in patients with primary lateral sclerosis (PLS) and using diffusion tensor (DT) magnetic resonance imaging (MRI) to determine the topographical distribution of microstructural white matter (WM) damage in patients with or without cognitive deficits.

Methods

DT MRI scans were obtained from 21 PLS patients and 35 age- and sex-matched healthy controls. All PLS patients underwent a comprehensive neuropsychological battery. Tract-based-spatial-statistics (TBSS) was used to perform a whole-brain voxel-wise analysis of fractional anisotropy (FA), axial, radial (radD) and mean diffusivity (MD).

Results

Ten PLS patients had abnormal scores in at least one neuropsychological test (PLS with cognitive deficits, PLS-cd). Compared with healthy controls and cognitively unimpaired PLS patients (PLS-cu), PLS-cd cases showed decreased FA and increased MD and radD in the corticospinal tract (CST), corpus callosum, brainstem, anterior limb of internal capsule, superior and inferior longitudinal fasciculi, fornix, thalamic radiations, and parietal lobes, bilaterally. Compared with healthy controls, PLS-cd patients showed further decreased FA and increased radD in the cerebellar WM, bilaterally. Compared with controls, PLS-cu patients showed decreased FA in the mid-body of corpus callosum. In PLS, executive and language test scores correlated with WM damage.

Conclusions

This is the first study evaluating the relationship between cognitive performance and WM tract damage in PLS patients. PLS can be associated with a multi-domain cognitive impairment. WM damage to interhemispheric, limbic and major associative WM tracts seem to be the structural correlate of cognitive abnormalities in these patients.     

Collective Electronic Excitations in Thin Ag Films on Ni(111)

The collective electronic excitations in thin Ag films deposited onto the Ni(111) surface were studied by high-resolution electron energy loss spectroscopy. A broad loss peak at 7.7 eV was assigned to the Ag multipole plasmon, in excellent agreement with calculations based on s-d polarization model. Ag multipole plasmon was excited only at grazing incidence. Furthermore, a strong dependence on the impinging energy exists. Multipole plasmon could be measured only for a very strict range of primary electron beam energies and it was excited by electrons scattered at a reflection plane located just underneath the jellium edge. Such mode was found to be dramatically more sensible to the state of the surface with respect to ordinary surface plasmon. Moreover, we report experimental evidence of interference effects in surface plasmon excitation.     

Advanced Glycation End Products in Infant Formulas Do Not Contribute to Insulin Resistance Associated with Their Consumption

Introduction

Infant formula-feeding is associated with reduced insulin sensitivity. In rodents and healthy humans, advanced glycation end product (AGE)-rich diets exert diabetogenic effects. In comparison with human breast-milk, infant formulas contain high amounts of AGEs. We assessed the role of AGEs in infant-formula-consumption-associated insulin resistance.

Methods

Total plasma levels of N^ε-(carboxymethyl)lysine (CML), AGEs-associated fluorescence (λ_ex = 370 nm/λ_em = 445 nm), soluble adhesion molecules, markers of micro- binflammation (hsCRP), oxidative stress (malondialdehyde, 8-isoprostanes) and leptinemia were determined, and correlated with insulin sensitivity in a cross-sectional study in 166 healthy term infants aged 3-to-14 months, subdivided according to feeding regimen (breast-milk- vs. infant formula-fed) and age (3-to-6-month-olds, 7-to-10-month-olds, and 11-to-14-month-old infants). Effects of the consumption of low- vs. high-CML-containing formulas were assessed. 36 infants aged 5.8±0.3 months were followed-up 7.5±0.3 months later.

Results

Cross-sectional study: 3-to-6-month-olds and 7-to-10-month-old formula-fed infants presented higher total plasma CML levels and AGEs-associated fluorescence (p<0.01, both), while only the 3-to-6-month-olds displayed lower insulin sensitivity (p<0.01) than their breast-milk-fed counterparts. 3-to-6-month-olds fed low-CML-containing formulas presented lower total plasma CML levels (p<0.01), but similar insulin sensitivity compared to those on high-CML-containing formulas. Markers of oxidative stress and inflammation, levels of leptin and adhesion molecules did not differ significantly between the groups. Follow-up study: at initial investigation, the breast-milk-consuming infants displayed lower total plasma CML levels (p<0.01) and AGEs-associated fluorescence (p<0.05), but higher insulin sensitivity (p<0.05) than the formulas-consuming infants. At follow-up, the groups did not differ significantly in either determined parameter.

Conclusions

In healthy term infants, high dietary load with CML does not play a pathophysiological role in the induction of infant formula-associated insulin resistance. Whether a high load of AGEs in early childhood affects postnatal programming remains to be elucidated.     

Altered White Matter Architecture in BDNF Met Carriers

Brain-derived neurotrophic factor (BDNF) modulates the pruning of synaptically silent axonal arbors. The Met allele of the BDNF gene is associated with a reduction in the neurotrophin''s activity-dependent release. We used diffusion-weighted imaging to construct structural brain networks for 36 healthy subjects with known BDNF genotypes. Through permutation testing we discovered clear differences in connection strength between subjects carrying the Met allele and those homozygotic for the Val allele. We trained a Gaussian process classifier capable of identifying the subjects'' allelic group with 86% accuracy and high predictive value. In Met carriers structural connectivity was greatly increased throughout the forebrain, particularly in connections corresponding to the anterior and superior corona radiata as well as corticothalamic and corticospinal projections from the sensorimotor, premotor, and prefrontal portions of the internal capsule. Interhemispheric connectivity was also increased via the corpus callosum and anterior commissure, and extremely high connectivity values were found between inferior medial frontal polar regions via the anterior forceps. We propose that the decreased availability of BDNF leads to deficits in axonal maintenance in carriers of the Met allele, and that this produces mesoscale changes in white matter architecture.     

Twenty-four-hour rhythm patterns of plasma melatonin in short-day and long-day breeders maintained under natural environmental conditions

ABSTRACT

Photoperiodic treatments have been of practical interest in controlling seasonal reproduction in sheep, goats and horses. Melatonin is the principal mediator of the environmental photoperiodic message. To investigate the intra- and inter-subject variability of melatonin 24 h rhythm, ten female Italian Saddle horses (8–10 yrs old, mean body weight 525 ± 30 kg), ten female Sarda breed sheep (2–3 yrs old, mean body weight 40.5 ± 2.8 kg) and ten female Sarda breed goats (3–4 yrs old, mean body weight 38.9 ± 4.1 kg), housed individually in a 4 × 4 m soundproof box equipped with 50 × 100 cm opening windows, were subjected to a natural photoperiod of the vernal equinox (sunrise 06:00 h; sunset 18:00 h). Blood samples were collected from each animal, every 3 h over a 48 h period starting at 00:00 h of day 1 and ending at 00:00 h of day 3. Plasma melatonin concentrations were determined by direct radioimmunoassay (MelatoninDirect RIA, Labor Diagnostika Nord GmbH, Nordhorn, Germany). The application of single cosinor method substantiated a circadian rhythm of melatonin with a nocturnal peak in all studied species. The application of two-way ANOVA on the rhythmic parameters indicated statistically significant differences between the three species in all of the cosinor analysis-derived parameters of MESOR, amplitude, acrophase and robustness of rhythm. Analyses of intra- and inter-subject variability indicate that organization of the melatonin 24 h rhythm is characterized by great accuracy of control within and between the individuals of a breed. In conclusion, features of the 24 h rhythm of melatonin among species; however, the 24 h rhythmicity of melatonin each species showed high stability within the various subjects and within the same subject. These findings must be taken into consideration when applying photoperiod and melatonin treatments for breeding purposes.