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.

Abstract

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.

     

The relationship between antioxidant compounds contents and antioxidant enzymes under water-deficit stress in the three Iranian cultivars of basil (<Emphasis Type="Italic">Ocimum basilicum</Emphasis> L.)

The current investigation was conducted to elucidate the potential modulatory functions of both enzymatic and non-enzymatic scavenging elements of three Iranian basil (Ocimum basilicum L.) cultivars in response to different water-deficit stress treatments [i.e., control (W1: 100 % FC), mild (W2: 75 % FC), moderate (W3: 50 % FC), and severe (W4: 25 % FC)]. In general, the growth parameters, viz., plant height, number of lateral branches, number of flowers in the inflorescence per plant, and dry and fresh weights of leaves and inflorescence followed by yield were considerably affected by water-deficit stress levels (p ≤ 0.05), though some fluctuations were observed among three cultivars. Under severe water-deficit stress (W4), total chlorophyll content overall increased, while a pronounced reduction in the carotenoid content was observed by boosting of water-deficit stress intensities. Apart from some quantitative variations, ROS-scavenging enzymes, such as SOD, CAT, APX, GPX, and PPO, exhibited different behaviors versus different levels of water-deficit stress in the basil cultivars, concluding that their modulation could be a cultivar-dependent mechanism and stress-dependent mechanism. Among different metabolites detected in the essential oil of basil cultivars, both methyl chavicol and squalene were superior in the cultivars 2 and 3, while in cultivar 1, linalool and squalene were the predominant constituents, under water deprivation conditions. Taking all the features studied here into consideration, presumably, cultivar 1 is qualified enough to nominate as the most tolerant basil cultivar, could be accordingly utilized as a promising source/material for breeding programs of basil under drought stress, and possibly other abiotic stresses.     

Terrestrial venomous animals,the envenomings they cause,and treatment perspectives in the Middle East and North Africa

The Middle East and Northern Africa, collectively known as the MENA region, are inhabited by a plethora of venomous animals that cause up to 420,000 bites and stings each year. To understand the resultant health burden and the key variables affecting it, this review describes the epidemiology of snake, scorpion, and spider envenomings primarily based on heterogenous hospital data in the MENA region and the pathologies associated with their venoms. In addition, we discuss the venom composition and the key medically relevant toxins of these venomous animals, and, finally, the antivenoms that are currently in use to counteract them. Unlike Asia and sub-Saharan Africa, scorpion stings are significantly more common (approximately 350,000 cases/year) than snakebites (approximately 70,000 cases/year) and present the most significant contributor to the overall health burden of envenomings, with spider bites being negligible. However, this review also indicates that there is a substantial lack of high-quality envenoming data available for the MENA region, rendering many of these estimates speculative. Our understanding of the venoms and the toxins they contain is also incomplete, but already presents clear trends. For instance, the majority of snake venoms contain snake venom metalloproteinases, while sodium channel–binding toxins and potassium channel–binding toxins are the scorpion toxins that cause most health-related challenges. There also currently exist a plethora of antivenoms, yet only few are clinically validated, and their high cost and limited availability present a substantial health challenge. Yet, some of the insights presented in this review might help direct future research and policy efforts toward the appropriate prioritization of efforts and aid the development of future therapeutic solutions, such as next-generation antivenoms.     

Combined metformin-salicylate treatment provides improved anti-tumor activity and enhanced radiotherapy response in prostate cancer; drug synergy at clinically relevant doses

BackgroundThere is need for well-tolerated therapies for prostate cancer (PrCa) secondary prevention and to improve response to radiotherapy (RT). The anti-diabetic agent metformin (MET) and the aspirin metabolite salicylate (SAL) are shown to activate AMP-activated protein kinase (AMPK), suppress de novo lipogenesis (DNL), the mammalian target of rapamycin (mTOR) pathway and reduce PrCa proliferation in-vitro. The purpose of this study was to examine whether combined MET+SAL treatment could provide enhanced PrCa tumor suppression and improve response to RT.MethodsAndrogen-sensitive (22RV1) and resistant (PC3, DU-145) PrCa cells and PC3 xenografts were used to examine whether combined treatment with MET+SAL can provide improved anti-tumor activity compared to each agent alone in non-irradiated and irradiated PrCa cells and tumors. Mechanisms of action were investigated with analysis of signaling events, mitochondria respiration and DNL activity assays.ResultsWe observed that PrCa cells are resistant to clinically relevant doses of MET. Combined MET + SAL treatment provides synergistic anti-proliferative activity at clinically relevant doses and enhances the anti-proliferative effects of RT. This was associated with suppression of oxygen consumption rate (OCR), activation of AMPK, suppression of acetyl-CoA carboxylase (ACC)-DNL and mTOR-p70^s6k/4EBP1 and HIF1α pathways. MET + SAL reduced tumor growth in non-irradiated tumors and enhanced the effects of RT.ConclusionMET+SAL treatment suppresses PrCa cell proliferation and tumor growth and enhances responses to RT at clinically relevant doses. Since MET and SAL are safe, widely-used and inexpensive agents, these data support the investigation of MET+SAL in PrCa clinical trials alone and in combination with RT.     

Chitosan magnetic nanoparticles for drug delivery systems

The potential of magnetic nanoparticles (MNPs) in drug delivery systems (DDSs) is mainly related to its magnetic core and surface coating. These coatings can eliminate or minimize their aggregation under physiological conditions. Also, they can provide functional groups for bioconjugation to anticancer drugs and/or targeted ligands. Chitosan, as a derivative of chitin, is an attractive natural biopolymer from renewable resources with the presence of reactive amino and hydroxyl functional groups in its structure. Chitosan nanoparticles (NPs), due to their huge surface to volume ratio as compared to the chitosan in its bulk form, have outstanding physico-chemical, antimicrobial and biological properties. These unique properties make chitosan NPs a promising biopolymer for the application of DDSs. In this review, the current state and challenges for the application magnetic chitosan NPs in drug delivery systems were investigated. The present review also revisits the limitations and commercial impediments to provide insight for future works.     

<Emphasis Type="Italic">Lactobacillus plantarum</Emphasis> as a Probiotic Potential from Kouzeh Cheese (Traditional Iranian Cheese) and Its Antimicrobial Activity

The aim of this study is to isolate and identify Lactobacillus plantarum isolates from traditional cheese, Kouzeh, and evaluate their antimicrobial activity against some food pathogens. In total, 56 lactic acid bacteria were isolated by morphological and biochemical methods, 12 of which were identified as Lactobacillus plantarum by biochemical method and 11 were confirmed by molecular method. For analyzing the antimicrobial activity of these isolates properly, diffusion method was performed. The isolates were identified by 318 bp band dedicated for L. plantarum. The isolated L. plantarum represented an inhibitory activity against four of the pathogenic bacteria and showed different inhibition halos against each other. The larger halos were observed against Staphylococcus aureus and Staphylococcus epidermidis (15 ± 0.3 and 14.8 ± 0.7 mm, respectively). The inhibition halo of Escherichia coli was smaller than that of other pathogen and some L. plantarum did not show any inhibitory activity against E. coli, which were resistant to antimicrobial compounds produced by L. plantarum. The isolated L. plantarum isolates with the antimicrobial activity in this study had strong probiotic properties. These results indicated the nutritional value of Kouzeh cheese and usage of the isolated isolates as probiotic strains.     

Oral poliovirus vaccine in management of recurrent aphthous stomatitis

Oral poliovirus vaccine (OPV) is reported to be effective in treatment of recurrent herpes simplex (RHS). According to our observation during recent years, OPV was not only effective in management of RHS but also in some patients with concomitant recurrent aphthous stomatitis (RAS) reducing its severity and frequency. The purpose of this study was to evaluate the efficacy of OPV in the management of RAS. In a longitudinal, case--control study 48 patients with RAS were recruited. Twenty patients received OPV and 28 patients received placebo. OPV was administered in a dose of 4 drops at monthly intervals for 3 months to the study group while the control group received placebo. The results were registered in 3 months after the last dose. Eight cases (40%) in the OPV group showed significant reduction in the duration of the ulcers, while no change was seen in the control group (P = 0.048). The frequency of recurrence of RAS was reduced in 13 cases (65%) in the OPV group, and in 6 cases (21.4%) of the placebo group (P = 0.006). The severity of attacks was reduced in 12 cases (60%) in the OPV group and in 4 cases (14.3%) in the placebo group (P = 0.008). In conclusion OPV appeared to be effective in the management of RAS.     

Epidemiology and Genetic Epidemiology of the Liver Function Test Proteins

Background

The liver function test (LFT) is among the most commonly used clinical investigations to assess hepatic function, severity of liver diseases and the effect of therapies, as well as to detect drug-induced liver injury (DILI).

Aims

To determine the relative contribution of genetic and environmental factors as well as test and quantify the effects of sex, age, BMI and alcohol consumption to variation in liver function test proteins - including alanine amino transaminase (ALT), Albumin, gamma glutamyl transpeptidase (GGT), total bilirubin, total protein, total globulin, aspartate transaminase (AST), and alkaline phosphotase (ALP) - using the classical twin model.

Methods

Blood samples were collected from a total of 5380 twin pairs from the TwinsUK registry. We measured the expression levels of major proteins associated with the LFT, calculated BMI from measured weight and height and questionnaires were completed for alcohol consumption by the twins. The relative contribution of genetic and environmental factors to variation in the LFT proteins was assessed and quantified using a variance components model fitting approach.

Results

Our results show that (1) variation in all the LFTs has a significant heritable basis (h² ranging from 20% to 77%); (2) other than GGT, the LFTs are all affected to some extent by common environmental factors (c² ranging from 24% to 54%); and (3) a small but significant proportion of the variation in the LFTs was due to confounding effects of age, sex, BMI, and alcohol use.

Conclusions

Variation in the LFT proteins is under significant genetic and common environmental control although sex, alcohol use, age and BMI also contribute significantly to inter-individual variation in the LFT proteins. Understanding the underlying genetic contribution of liver function tests may help the interpretation of their results and explain wide variation among individuals.     

Enhancement of the Bioremediation of Pyrene-Contaminated Soils Using a Hematite Nanoparticle-based Modified Fenton Oxidation in a Sequenced Approach

The effect of modified Fenton oxidation using synthesized hematite nanoparticles and sodium pyrophosphate as a chelating agent was investigated for the pretreatment of pyrene-contaminated soil in a sequence with bioremediation. Synthesized hematite nanoparticles comprised hematite according to X-ray diffraction (XRD) analysis, with particle sizes ranging between 28 and 55 nm. Three pyrene-degrading bacteria, Bacillus cereus, Acidovorax wohlfahrtii, and Bacillus thuringiensis, were isolated from hydrocarbon-contaminated soil and used as inoculums for the bioremediation. A sequence of modified Fenton oxidation-bioremediation using a synthesized hematite nanoparticles dosage of 30 mM and H₂O₂ concentration of 300 mM significantly enhanced the pyrene removal rate to 96%, 87%, and 82% compared to 88%, 59%, and 37%, which were obtained during the bioremediation alone for synthetically fresh, aged, and naturally contaminated soil with initial pH 7, respectively. The results of kinetic studies indicated that modified Fenton oxidation of pyrene-contaminated soil was best fitted with a pseudo-first order kinetic model. Consequently, a sequence of modified Fenton-bioremediation can effectively remediate polycyclic aromatic hydrocarbon-contaminated sites in a shorter reaction time than bioremediation alone.     

Oxytocin infusion increases charitable donations regardless of monetary resources

This study examined if the prosocial effects of oxytocin (OT) extend from individuals to a generalized other who is in need. Participants played a series of economic games to earn money and were presented with an opportunity to donate a portion of their earnings to charity. OT did not significantly increase the decision to donate, but among the 36% of participants who did donate, people infused with OT were found to donate 48% more to charity than those given a placebo. The amount of money earned in the experiment had no effect on whether or not a donation was made or the size of a donation. This is the first study showing that OT increases generosity in unilateral exchanges directed toward philanthropic social institutions, as opposed to immediate benefits directed at individuals or groups.