Rice diversity panel provides accurate genomic predictions for complex traits in the progenies of biparental crosses involving members of the panel

KEY MESSAGE

Rice breeding programs based on pedigree schemes can use a genomic model trained with data from their working collection to predict performances of progenies produced through rapid generation advancement. So far, most potential applications of genomic prediction in plant improvement have been explored using cross validation approaches. This is the first empirical study to evaluate the accuracy of genomic prediction of the performances of progenies in a typical rice breeding program. Using a cross validation approach, we first analyzed the effects of marker selection and statistical methods on the accuracy of prediction of three different heritability traits in a reference population (RP) of 284 inbred accessions. Next, we investigated the size and the degree of relatedness with the progeny population (PP) of sub-sets of the RP that maximize the accuracy of prediction of phenotype across generations, i.e., for 97 F5-F7 lines derived from biparental crosses between 31 accessions of the RP. The extent of linkage disequilibrium was high (r 2 = 0.2 at 0.80 Mb in RP and at 1.1 Mb in PP). Consequently, average marker density above one per 22 kb did not improve the accuracy of predictions in the RP. The accuracy of progeny prediction varied greatly depending on the composition of the training set, the trait, LD and minor allele frequency. The highest accuracy achieved for each trait exceeded 0.50 and was only slightly below the accuracy achieved by cross validation in the RP. Our results thus show that relatively high accuracy (0.41-0.54) can be achieved using only a rather small share of the RP, most related to the PP, as the training set. The practical implications of these results for rice breeding programs are discussed.

Multipoint Measurements of the Electron Jet of Symmetric Magnetic Reconnection with a Moderate Guide Field

We report observations from the Magnetospheric Multiscale (MMS) satellites of the electron jet in a symmetric magnetic reconnection event with moderate guide field. All four spacecraft sampled the ion diffusion region and observed the electron exhaust. The observations suggest that the presence of the guide field leads to an asymmetric Hall field, which results in an electron jet skewed towards the separatrix with a nonzero component along the magnetic field. The jet appears in conjunction with a spatially and temporally persistent parallel electric field ranging from -3 to -5  mV/m, which led to dissipation on the order of 8  nW/m^{3}. The parallel electric field heats electrons that drift through it, and is associated with a streaming instability and electron phase space holes.

Blue-white screening as a new readout for deoxyribozyme activity in bacterial cells

Demonstration of 10–23 deoxyribozyme activity in viable E. coli using blue-white screening as the readout system.

Dataset of plasmid DNA extraction using different magnetic nanoparticles (MNPs)

In this dataset we integrated figures related to bacterial transformation using pBI121 plasmid and complementary analysis for magnetic nanoparticles (MNPs) characterizations. The structural map of pBI121 plasmid was drawn by Vector NTI software using the complete sequence of binary vector pBI121. Escherichia coli bacteria transformed using pBI121 plasmid and were grown on the selection media containing kanamycin.

MNPs were characterized by energy dispersive spectroscopy (EDS) and transmission electron microscopy (TEM). Finally, the overall efficiency of different MNPs (Fe₃O₄, Fe₃O₄/SiO₂, Fe₃O₄/SiO₂/TiO₂) in plasmid DNA isolation was compared using gel electrophoresis analysis. The data supplied in this article supports the accompanying publication “Comparative study of three magnetic nano-particles (FeSO₄, FeSO₄/SiO₂, FeSO₄/SiO₂/TiO₂) in plasmid DNA extraction” (H. Rahnama, A. Sattarzadeh, F. Kazemi, N. Ahmadi, F. Sanjarian, Z. Zand, 2016) [1].

Kidney Blow Out Due to Inguinal Herniation of the Ureter in an Infant

Ureteroinguinal herniation is a rare event, usually diagnosed during the surgical repair of inguinal hernias. Here, we describe the first case of a kidney blow out due to this condition in a male infant.

Intranasal corticosteroids do not affect intraocular pressure or lens opacity: a systematic review of controlled trials

BACKGROUND

Intranasal corticosteroids (INCS) are prescribed for the long-term prophylactic treatment of inflammatory upper airway conditions. Although some systemic absorption can occur via topical routes, the clinical relevance is controversial. The effects of orally administered corticosteroids on intraocular pressure (IOP) and lens opacity (LO) are well established, but the impact of the INCS is less well defined. This study aims to systematically review the literature for evidence of adverse occular events with INCS use.

METHODOLOGY

A systematic review of literature from Medline and Embase databases (January 1974 to 21st of November 2013) was performed. Using the PRISMA guidelines, all controlled clinical trials of patients using INCS, that reported original measures of IOP, LO, glaucoma or cataract incidences were included. Studies with adjuvant administration of oral, inhaled and intravenous steroids were excluded.

RESULTS

665 articles were retrieved with 137 were considered for full-text review. Of these, 116 (85%) were literature reviews and two were case reports. 19 studies (10 RCTs, 1 case-control, 8 case series) were included for the qualitative review, of which 18 reported data on IOP and 10 on cataract/LO. None (n=0) of the 10 RCT reporting data on glaucoma or IOP demonstrated changes in IOP compared to control. Also none (n=0) of the 6 RCTs reporting cataract or lens opacity demonstrated changes compared to control.

CONCLUSION

Data from studies with low levels of bias, do not demonstrate a clinically relevant impact of INCS on neither ocular pressure, glaucoma, lens opacity nor cataract formation.

Depression Levels among Mothers of Children with Leukemia

BACKGROUND

The aim of the study was to evaluate the depression levels in mothers of children with leukemia.

MATERIALS AND METHODS

This single centred, cross-sectional study was conducted among mothers of children with leukemia at the Hematology and Oncology research center, Baghaie-Pour clinic in Yazd City during February through December, 2013. The study sample included 58 mothers with 1-12 year old children with the diagnosis or treated at the Shahid Sadoughi hospital. Socio-demographic characteristics were gathered using a socio-demographic form and Beck Depression Inventory (BDI) was applied to all mothers to assess symptoms of depression. All variables that could potentially impact dependent outcome measures of the BDI were analyzed. These factors were mothers' age, mothers' education, and socioeconomic status of the family, gender of child.

RESULTS

The analysis revealed that mothers of children leukemia had a severe level of depression (p=0.01). 41 participants (70.6%) indicated their current depressive symptoms as being in the severe range, 12 participants (20.6%) in the moderate range, and 5 participants (8.6%) in the mild range or no depression. There was an inverse correlation between the educational level of the mothers and the heads of household, their occupational status, their marital status, their socio-economic condition and depression (p≤0.05). The depression scores of the mothers of patients were higher than those of the controls.

CONCLUSION

Depression ideation is common among mothers of children with leukemia. There are strong associations with socio-economic condition and high depression levels.

Clinical and morphopathological characteristics of an enzootic occurrence of acute coenurosis (Coenurus cerebralis) in a sheep herd

In this study, 30 sheep from a flock suddenly showed acute neurological symptoms associated with more than 30 % mortality. At necropsy, thickening associated with congestion and turbidity of meningeal membranes particularly on cerebellum, focal to multifocal necrotic areas and whitish spots measuring 1 to 3 cm in diameter were observed in the cortex of cerebrum and cerebellum. Grossly, numerous white tracts were also observed in the myocardium. Histopathologically, the cross sections of coenurus larvae associated with necrotic suppurative meningoencephalitis were observed. Multiple necrotic areas were also observed in the gray matter of cerebellum due to migration of the larvae with an extensive infiltration of eosinophils and neutrophils. In the heart, multifocal granulomatous myocarditis was diagnosed. No growth was seen in bacterial cultures of the brain and heart. Also, no bacteria were seen in these tissues stained with Ziehl-Neelsen and Brown-Brenn Gram stain. On basis of gross and histopathologic lesions, acute coenurosis was diagnosed. Unlike chronic coenurosis, acute form of the disease rarely reported in sheep.

Tissue distribution of infectious pancreatic necrosis virus serotype Sp in naturally infected cultured rainbow trout, Oncorhynchus mykiss (Walbaum): an immunohistochemical and nested-PCR study

This study investigates the occurrence and distribution pattern of infectious pancreatic necrosis virus (IPNV) within the pancreas, liver, kidney and spleen of naturally infected cultured rainbow trout, Oncorhynchus mykiss (Walbaum), using immunohistochemistry (IHC). A nested PCR was also employed to confirm the presence of the virus in the pooled tissues of the specimens. All the examined tissues except spleen were immunohistochemically positive for IPNV, but staining intensity and distribution pattern varied. The kidney tubules had the most intense and widespread staining by IHC, indicating a specific tissue tropism at least for this particular serotype. The nucleotide sequence had the greatest identity with the Sp serotype confirming the presence of the nucleic acid of IPNV in the pooled tissues. Based on the present findings, it could be concluded that the absence of lesions consistent with infectious pancreatic necrosis (IPN) disease in the H&E-stained sections cannot rule out the presence of the IPNV, and the use of an alternative rapid confirmatory method such as IHC with formalin-fixed, paraffin-embedded tissue sections is helpful for the final diagnosis of IPN in rainbow trout.

Targeted association analysis identified japonica rice varieties achieving Na(+)/K (+) homeostasis without the allelic make-up of the salt tolerant indica variety Nona Bokra

During the last decade, a large number of QTLs and candidate genes for rice tolerance to salinity have been reported. Using 124 SNP and 52 SSR markers, we targeted 14 QTLs and 65 candidate genes for association mapping within the European Rice Core collection (ERCC) comprising 180 japonica accessions. Significant differences in phenotypic response to salinity were observed. Nineteen distinct loci significantly associated with one or more phenotypic response traits were detected. Linkage disequilibrium between these loci was extremely low, indicating a random distribution of favourable alleles in the ERCC. Analysis of the function of these loci indicated that all major tolerance mechanisms were present in the ERCC although the useful level of expression of the different mechanisms was scattered among different accessions. Under moderate salinity stress some accessions achieved the same level of control of Na(+) concentration and Na(+)/K(+) equilibrium as the indica reference variety for salinity tolerance Nona Bokra, although without sharing the same alleles at several loci associated with Na(+) concentration. This suggests (a) differences between indica and japonica subspecies in the effect of QTLs and genes involved in salinity tolerance and (b) further potential for the improvement of tolerance to salinity above the tolerance level of Nona Bokra, provided the underlying mechanisms are complementary at the whole plant level. No accession carried all favourable alleles, or showed the best phenotypic responses for all traits measured. At least nine accessions were needed to assemble the favourable alleles and all the best phenotypic responses. An effective strategy for the accumulation of the favourable alleles would be marker-assisted population improvement.

Pulmonary myxoma in a sheep

Pulmonary myxomas are rare in domestic animals and only two cases have been reported previously in sheep. An 8 x 6 x 4 cm mass was detected in the diaphragmatic lobe of the right lung of a 4-year-old Persian Karakul ewe. The mass was well demarcated, multilobulated, soft in consistency and white in colour. The cut surface exuded a mucoid substance and a distinct capsule was evident. Microscopically, the tumour comprised a hypocellular myxomatous matrix, rich in acid mucopolysaccharides, with scattered spindle-shaped or stellate cells. These cells had uniform, oval-shaped nuclei without visible nucleoli and expressed vimentin and S100 on immunohistochemical examination. These gross, microscopical and immunohistochemical features are characteristics of myxoma.

Measurement of coronary artery calcification by electron beam computerized tomography in persons with chronic spinal cord injury: evidence for increased atherosclerotic burden

BACKGROUND/OBJECTIVE

Individuals with spinal cord injury (SCI) have been reported to have an increased prevalence of premature cardiovascular disease. Whether the increased risk of disease is owing to clustering of traditional cardiac risk factor or is over and above that predicted by risk factors was addressed.

METHODS

Ninety-one persons with chronic SCI were studied for subclinical atherosclerosis. Cardiac risk factors and coronary artery calcium (CAC) was compared to matched non-SCI controls. The 273 controls were 3:1 matched for age, gender, ethnicity and risk factors and were drawn from a national database of over 30,000 asymptomatic persons undergoing coronary scanning.

RESULTS

Seventy-six men and 15 women were studied. Average age was 49.7+/-12 years. Duration of injury was 19.7+/-10 years. The ethnicity of the study cohort included 36% Caucasian, 49% Latino, 10% African American, and 5% other. The mean calcium score of the SCI group was significantly greater than the control group (75+/-218 versus 28+/-104, P<0.001). The prevalence of any CAC score was greater in the SCI population than the control population (51 versus 39%, P<0.05), as was CAC score >100 (16 versus 7%, P<0.01). Women with SCI had a significantly lower CAC score than men (mean score: 12 versus 86, P<0.01).

CONCLUSION

Patients with SCI were shown to have greater atherosclerotic burden than able-bodied controls. Of note, and unexplained, this finding is beyond that explained by the clustering of traditional risk factors. On the basis of these findings, increased attention should be directed toward the prevention of coronary heart disease in those with SCI.

Characterization of Echinococcus granulosus isolates from human, sheep and camel in Iran

In the present study, Echinoccocus granulosus isolates collected from human, sheep and camel samples in Iran were characterized based on rostellar hook morphology of protoscoleces as well as PCR-RFLP. Morphological study on human and animal isolates showed the presence of two distinct strains of the parasite, one in sheep and the other one in camels. In this regard, rostellar hook of sheep isolates were significantly different from those of camel origin, meanwhile human isolates were found to be similar to those isolated from sheep. Molecular analysis of the ITS1 region of rDNA derived from human, sheep and camel isolates were in agreement with the morphological findings. Based on the PCR-RFLP method, the sheep and human isolates appeared to pertain to the same genotype and the camel isolates were appeared to pertain to a different genotype.

Naltrexone for alcohol-dependent patients

BACKGROUND

Clinical trials have shown that naltrexone 50 mg/day reduces alcohol consumption and relapse rates in alcohol dependents.

AIM

To investigate the efficacy of 50mg/day dose of naltrexone in the maintenance of alcohol-dependent subjects over a 36-week treatment period.

METHODS

Subjects were randomised into two equal groups, consisting of 116 male alcohol-dependent patients who met the DSM-IV criteria for alcohol dependence and were seeking treatment. The participants received naltrexone or placebo at a dose of 50 mg/day and were treated in an outpatient clinic, offering a weekly 0.5-hour individual counselling session. Days retained in treatment were measured.

RESULTS

Forty-one participants (35.3%) completed the 36-week study. Completion rates by group were 44.8% for the 50 mg naltrexone group and 25.9% for the placebo group (chi2=4.56, DF=1, 2-sided significance=0.033).

CONCLUSION

The results support the efficacy and safety of naltrexone for outpatient treatment of alcohol-dependent individuals in Iran.

Effects of iodized salt consumption on goiter prevalence in Isfahan: the possible role of goitrogens

OBJECTIVE

To evaluate the success of the Iranian Iodine Deficiency Disorders Committee in achieving World Health Organization (WHO) goals for reducing the prevalence of goiter in children by adding iodine to table salt beginning in 1989.

METHODS

In 1997, 8,000 male and female 6- to 18-year-old students were selected by cluster sampling in schools of Isfahan. Their thyroids were examined by four endocrinologists, and goiter was staged on the basis of the WHO classification. As an index of iodine consumption, urinary iodine concentrations were measured in 3,000 students.

RESULTS

Goiter was observed in 62% of the students. Of the overall study group, 94% had sufficient iodine consumption (urinary iodine concentration of 10.0 microg/dL or more). Of those students who had sufficient iodine intake, 63.2% had goiter. Of the 6% of students with iodine deficiency, 5% had mild, 0.9% had moderate, and only 0.1% had severe iodine deficiency. Goiter was absent in half of the students with severe iodine deficiency. The prevalence of goiter in 6- to 10-year-old children was 65%.

CONCLUSION

Despite sufficient iodine intake, the prevalence of goiter is still high in Isfahan City. Apparently, either this high prevalence has no relationship to iodine deficiency and possibly other unknown goitrogens are involved in the pathogenesis of goiter in Isfahan or the period of iodine intake has been too brief to affect thyroid sizes. Inasmuch as goiter prevalence is also high in the 6- to 10-year-old children, who have had iodized salt available for most of their lives, the second option is less probable. Another possibility is an increased rate of autoimmune thyroid diseases (because of iodine repletion) that resemble goiter during their early stages.