Use of an expressed sequence tag-based method for single nucleotide polymorphism identification and discrimination of Citrus species and cultivars

Sweet orange [Citrus sinensis (L.) Osbeck] represents the most important Citrus species, followed by clementine (C. clementina Hort. ex Tan.). Citrus species and genotypes are difficult to recognize as they have a moderate level of diversity due to nucellar selection, vegetative propagation and origin by single spontaneous mutation. Despite the large number of available sequences and the existence of a draft assembly of sweet orange and clementine, there are currently no single nucleotide polymorphism (SNP) databases for Citrus species. For this purpose, the QualitySNP software was used to discover SNPs in 19 Citrus species starting from 540,000 expressed sequence tags (ESTs) assembled in 52,000 contigs. The vast majority of ESTs, contigs and SNPs were found in C. clementina and C. sinensis: 4,400 out of 16,000 contigs (27 %) of C. clementina and 4,100 out of 17,000 contigs (24 %) of C. sinensis contained putative SNPs. A total of 3,634 sequences were associated with enzymes belonging to 121 metabolic KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, among which the secondary metabolite pathway was the most represented. A total of 163 SNPs from 52 contigs and genes of specific functional categories were validated and 81 polymorphic sites were found. Thirty-seven selected SNPs, validated by Sanger sequencing, confirmed that polymorphisms were mainly between species, while poor within-species variability was discovered. This work provides a collection of 15,879 putative SNP markers that could be exploited by the Citrus community. Furthermore, the validated SNPs associated with specific genes could be used for functional genetic studies in germplasm diversity analysis, mapping and breeding.     

Structural basis of phosphoinositide binding to kindlin-2 protein pleckstrin homology domain in regulating integrin activation

Kindlins are a subclass of FERM-containing proteins that have recently emerged as key regulators of integrin receptor activation and signaling. As compared with the conventional FERM domain, the kindlin FERM domain contains an inserted pleckstrin homology (PH) domain that recognizes membrane phosphoinositides, including phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3). Using NMR spectroscopy, we show that PIP3 site-specifically binds to kindlin-2 PH with substantial chemical shift changes that are much larger than PIP2. This suggests an enhanced association of kindlin-2 with membrane as mediated by PIP3 upon its conversion from PIP2 by phosphoinositide-3 kinase, a known regulator of integrin activation. We determined the NMR structure of the kindlin-2 PH domain bound to the head group of PIP3, inositol 1,3,4,5-tetraphosphate (IP4). The structure reveals a canonical PH domain fold, yet with a distinct IP4 binding pocket that appears highly conserved for the kindlin family members. Functional experiments demonstrate that although wild type kindlin-2 is capable of cooperating with integrin activator talin to induce synergistic integrin α(IIb)β(3) activation, this ability is significantly impaired for a phosphoinositide binding-defective kindlin-2 mutant. These results define a specific PIP3 recognition mode for the kindlin PH domain. Moreover, they shed light upon a mechanism as to how the PH domain mediates membrane engagement of kindlin-2 to promote its binding to integrin and cooperation with talin for regulation of integrin activation.     

The Reg3α (HIP/PAP) Lectin Suppresses Extracellular Oxidative Stress in a Murine Model of Acute Liver Failure

MethodsPrimary hepatocytes stressed with the reactive oxygen species (ROS) inducers TNFα and H₂O₂ were incubated with a recombinant Reg3α protein. ALF was induced in C57BL/6J mice by an anti-CD95 antibody. Livers and primary hepatocytes were harvested for deoxycholate separation of cellular and extracellular fractions, immunostaining, immunoprecipitation and malondialdehyde assays. Fibrin deposition was studied by immunofluorescence in frozen liver explants from patients with ALF.ResultsFibrin deposition occurs during experimental and clinical acute liver injuries. Reg3α bound the resulting transient fibrin network, accumulated in the inflammatory extracellular matrix (ECM), greatly reduced extracellular ROS levels, and improved cell viability. Hepatocyte treatment with ligands of death receptors, e.g. TNFα and Fas, resulted in a twofold increase of malondialdehyde (MDA) level in the deoxycholate-insoluble fractions. Reg3α treatment maintained MDA at a level similar to control cells and thereby increased hepatocyte survival by 35%. No antioxidant effect of Reg3α was noted in the deoxycholate-soluble fractions. Preventing fibrin network formation with heparin suppressed the prosurvival effect of Reg3α.ConclusionsReg3α is an ECM-targeted ROS scavenger that binds the fibrin scaffold resulting from hepatocyte death during ALF. ECM alteration is an important pathogenic factor of ALF and a relevant target for pharmacotherapy.     

The Effect of VoorZorg,the Dutch Nurse-Family Partnership,on Child Maltreatment and Development: A Randomized Controlled Trial

Background

Child maltreatment is a great public health concern that has long-term mental and physical health consequences and can result in death. We studied the effect of a nurse home visiting program on child maltreatment among young disadvantaged families in the Netherlands. This study is the first to investigate the effects of this program outside of the United States.

Methods

We conducted a single blind, parallel-group, randomized controlled trial that compared usual care with the nurse home visitation program, which began during pregnancy and continued until the children’s second birthdays, in 460 disadvantaged women who were pregnant for the first time and <26 years of age. The primary outcome was the existence of a report about the child from a child protecting services agency (CPS reports). Secondary outcome measures included home environment and child behavior.

Results

Two hundred twenty-three participants were assigned to the control group, and 237 were assigned to the intervention group. Three years after birth, 19% of the children in the control group had a CPS report. The 11 percent of children in the intervention group with CPS files was significantly lower (relative risk 0.91, p-value 0.04). At 24 months, the intervention group scored significantly better on the IT-HOME. At 24 months after birth, the children in the intervention group exhibited a significant improvement in internalizing behavior (relative risk 0.56, p-value 0.04) but no evidence of a difference from the control group in externalizing behavior (relative risk 0.71, p-value 0.12).

Conclusion

The number of CPS reports for the intervention group was significantly lower than that of the control group. Additionally, the long-term home environments were improved and internalizing behaviors of the children were lower in the intervention group.

Trial Registration

Dutch Trial Register NTR854     

Microbiological quality of wheat flour consumed in Morocco

Cereal products (soft and hard wheat) are a basic staple food in the Moroccan diet. A total of 60 samples of two types of wheat flours used for human consumption were collected; 30 samples among this collection were obtained from various households using Moroccan varieties of wheat produced in traditional flour mills. The rest of the samples were purchased from retail wheat flour sources in the Rabat and Sale city markets. Standard plate counts (SPC), total and faecal coliforms, Clostridium, Salmonella spp., Shigella spp., Staphylococcus aureus, Listeria monocytogenes, yeast, lactic acid bacteria, and molds, were carried out to assess the microbiological quality of wheat flour. Microbiological interpretation of the criteria was performed according to standards implemented by the Codex Alimentarius Commission. Most frequent counts, in traditional and industrial wheat flour, were total aerobic mesophilic bacteria with an average 4 × 104 and 2.5 × 104 cfu/g, respectively. The results showed higher coliform and fungi counts in house than in commercial samples. Pathogenic flora as Salmonella spp., Shigella spp., S. aureus, L. monocytogenes, and Clostridium were not detected in all investigated samples. Bacterial strains isolated from both flours belong to the following genera: Enterobacter spp., Serratia spp., Klebsiella spp., Pantoea spp., Leclercia spp., Proteus spp. The most frequent genus of the investigated isolates was Aspergillus (81 %). Microbial counts were lower than the limit laid down in the Codex Alimentarius, attributing to these flours a satisfactory microbiological quality.     

Reversal by green light of blue light-stimulated stomatal opening in intact, attached leaves of Arabidopsis operates only in the potassium-dependent, morning phase of movement

Green light reversal of blue light-stimulated stomatal opening was discovered in isolated stomata. The present study shows that the response also occurs in stomata from intact leaves. Arabidopsis thaliana plants were grown in a growth chamber under blue, red and green light. Removal of the green light opened the stomata and restoration of green light closed them to baseline values under experimental conditions that rule out a mesophyll-mediated effect. Assessment of the response to green light over a daily time course showed that the stomatal sensitivity to green light was observed only in the morning, which coincided with the use of potassium as a guard cell osmoticum. Sensitivity to green light was absent during the afternoon phase of stomatal movement, which was previously shown to be dominated by sucrose osmoregulation in Vicia faba. Hence, the shift away from potassium-based osmoregulation in guard cells is further postulated to entail a shift from blue light to photosynthesis as the primary component of the stomatal response to light. Stomata from intact leaves of the zeaxanthin-less, npq1 mutant of Arabidopsis failed to respond to the removal or restoration of green light in the growth chamber, or to short, high fluence pulses of blue or green light. These data confirm previous studies showing that npq1 stomata are devoid of a specific blue light response. In contrast, stomata from intact leaves of phot1 phot2 double mutant plants had a reduced but readily detectable response to the removal of green light and to blue and green pulses.     

Germination responses of Spartidium saharae (Coss. & Dur.) Pomel (Fabaceae) to temperature and salinity

Spartidium saharae is an endemic species of the Saharo-Arabian region. It is a tall shrub widely distributed in many sandy habitats including desert dunes and sandy systems in south-western part of Tunisia, where water and salinity are serious constraints. Laboratory experiments were carried out to assess temperature and salinity effects on seed germination. The seed germination responses were determined in complete darkness over a wide range of temperatures and salinities. Germination was inhibited by either an increase or decrease in temperature from the optimal temperature range (15–20°C). Highest germination percentages were obtained under nonsaline conditions and an increase in NaCl concentrations progressively inhibited seed germination. An interaction between salinity and temperature yielded no germination at 200 m m NaCl.     

Simulated microgravity promotes nitric oxide-supported angiogenesis via the iNOS-cGMP-PKG pathway in macrovascular endothelial cells

Angiogenesis is a physiological process involving the growth of blood vessel in response to specific stimuli. The present study shows that limited microgravity treatments induce angiogenesis by activating macrovascular endothelial cells. Inhibition of nitric oxide production using pharmacological inhibitors and inducible nitric oxide synthase (iNOS) small interfering ribo nucleic acid (siRNA) abrogated microgravity induced nitric oxide production in macrovascular cells. The study further delineates that iNOS acts as a molecular switch for the heterogeneous effects of microgravity on macrovascular, endocardial and microvascular endothelial cells. Further dissection of nitric oxide downstream signaling confirms that simulated microgravity induces angiogenesis via the cyclic guanosine monophosphate (cGMP)-PKG dependent pathway.     

Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long‐distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic–Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b‐RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic–Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic–Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic–Ionian locations indicates species‐specific differences in genetic connectivity patterns and warns against generalizing single‐species results to the entire community of rocky shore habitats.