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Adequate silicon fertilization greatly boosts rice yield and mitigates biotic and abiotic stress, and improves grain quality through lowering the content of cadmium and inorganic arsenic. This review on silicon dynamics in rice considers recent advances in our understanding of the role of silicon in rice, and the challenges of maintaining adequate silicon fertility within rice paddy systems. Silicon is increasingly considered as an element required for optimal plant performance, particularly in rice. Plants can survive with very low silicon under laboratory/glasshouse conditions, but this is highly artificial and, thus, silicon can be considered as essential for proper plant function in its environment. Silicon is incorporated into structural components of rice cell walls were it increases cell and tissue rigidity in the plant. Structural silicon provides physical protection to plants against microbial infection and insect attack as well as reducing the quality of the tissue to the predating organisms. The abiotic benefits are due to silicon’s effect on overall organ strength. This helps protect against lodging, drought stress, high temperature (through efficient maintenance of transpiration), and photosynthesis by protecting against high UV. Furthermore, silicon also protects the plant from saline stress and against a range of toxic metal stresses (arsenic, cadmium, chromium, copper, nickel and zinc). Added to this, silicon application decreases grain concentrations of various human carcinogens, in particular arsenic, antimony and cadmium. As rice is efficient at stripping bioavailable silicon from the soil, recycling of silicon rich rice straw biomass or addition of inorganic silicon fertilizer, primarily obtained from iron and steel slag, needs careful management. Silicon in the soil may be lost if the silicon-cycle, traditionally achieved via composting of rice straw and returning it to the land, is being broken. As composting of rice straw and incorporation of composted or non-composted straw back to land are resource intensive activities, these activities are declining due to population shifts from the countryside to cities. Processes that accelerate rice straw composting, therefore, need to be identified to aid more efficient use of this resource. In addition, rice genetics may help address declining available silicon in paddy soils: for example by selecting for characteristics during breeding that lead to an increased ability of roots to access recalcitrant silicon sources from soil and/or via selection for traits that aid the maintenance of a high silicon status in shoots. Recent advances in understanding the genetic regulation of silicon uptake and transport by rice plants will aid these goals. [ABSTRACT FROM AUTHOR]

The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate tolerance in wild grass Holcus lanatus genotypes screened from the same habitat., De novo transcriptome sequencing, RNAseq (RNA sequencing) and single nucleotide polymorphism ( SNP) calling were conducted on RNA extracted from H. lanatus. Roche 454 sequencing data were assembled into c. 22 000 isotigs, and paired-end Illumina reads for phosphorus-starved (P−) and phosphorus-treated ( P+) genovars of tolerant ( T) and nontolerant ( N) phenotypes were mapped to this reference transcriptome., Heatmaps of the gene expression data showed strong clustering of each P+/ P− treated genovar, as well as clustering by N/ T phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between N and T phenotypes and 258 between P+ and P− treated plants. SNPs and transcript expression that systematically differed between N and T phenotypes had regulatory function, namely proteases, kinases and ribonuclear RNA-binding protein and transposable elements., A single gene for arsenate tolerance led to distinct phenotype transcriptomes and SNP profiles, with large differences in upstream post-translational and post-transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism per se. [ABSTRACT FROM AUTHOR]

Background: We have recently identified a number of Quantitative Trait Loci (QTL) contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA) muscle of each strain by RNA-Seq. Results: 13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN). The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10) residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs) underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p<0.03). Conclusion: Thus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs. [ABSTRACT FROM AUTHOR]

The host genotype has been proposed to contribute to individually composed bacterial communities in the gut. To provide deeper insight into interactions between gut bacteria and host, we associated germ-free C3H and C57BL/10 mice with intestinal bacteria from a C57BL/10 donor mouse. Analysis of microbiota similarity between the animals with denaturing gradient gel electrophoresis revealed the development of a mouse strain-specific microbiota. Microarray-based gene expression analysis in the colonic mucosa identified 202 genes whose expression differed significantly by a factor of more than 2. Application of bioinformatics tools demonstrated that functional terms including signaling/secretion, lipid degradation/catabolism, guanine nucleotide/guanylate binding and immune response were significantly enriched in differentially expressed genes. We had a closer look at the 56 genes with expression differences of more than 4 and observed a higher expression in C57BL/10 mice of the genes coding for Tlr1 and Ang4 which are involved in the recognition and response to gut bacteria. A higher expression of Pla2g2a was detected in C3H mice. In addition, a number of interferon-inducible genes were higher expressed in C3H than in C57BL/10 mice including Gbp1, Mal, Oasl2, Ifi202b, Rtp4, Ly6g6c, Ifi27l2a, Usp18, Ifit1, Ifi44, and Ly6g indicating that interferons may play an essential role in microbiota regulation. However, genes coding for interferons, their receptors, factors involved in interferon expression regulation or signaling pathways were not differentially expressed between the two mouse strains. Taken together, our study confirms that the host genotype is involved in the establishment of host-specific bacterial communities in the gut. Based on expression differences after colonization with the same bacterial inoculum, we propose that Pla2g2a and interferon-dependent genes may contribute to this phenomenon. [ABSTRACT FROM AUTHOR]

Highlights: [•] This paper reports a detailed examination of how a polymorphism in arsenate tolerance in grasses from non-arsenic contaminated environments is maintained due to phosphate fertilization. [•] This polymorphism will be of wide interest as it relates to phenotypic responses to phosphate, a fertiliser that is fast running out in a global context as it is a limited natural resource. [•] The report details that the polymorphism is present in many more grasses, suggesting that the phenomenon studied widely occurs in the plant kingdom. [Copyright &y& Elsevier]

Dietary patterns provide a comprehensive assessment of food consumption, including essential nutrients and potential exposure to environmental contaminants. While pro-vegetarian (PVG) dietary patterns have shown health benefits in adults, their effects on children are less well studied. This study aims to explore the association between children's adherence to the most common PVG dietary patterns and their exposure to metals, assessed through urine concentration. In our study, we included a population of 723 children aged 4-5-years from the INfancia y Medio Ambiente (INMA) cohort in Spain. We calculated three predefined PVG dietary patterns, namely general (gPVG), healthful (hPVG), and unhealthful (uPVG), using dietary information collected through a validated Food Frequency Questionnaire. Urinary concentrations of various essential and heavy metals (Co, Cu, Zn, Se, Mo, Pb, and Cd) were measured using mass spectrometry. Additionally, urinary arsenic speciation, including arsenobetaine (AsB), dimethylarsinic acid (DMA), monomethylarsonic acid (MMA), and inorganic arsenic (iAs), was measured. The sum of urinary MMA and iAs was used to assess iAs exposure. We estimated primary (PMI) and secondary iAs methylation (SMI) indices. To explore the association between PVG dietary patterns in quintiles and metal exposure, we utilized multiple-adjusted linear regression models and the quantile g-computation approach. Compared with the lowest quintile, participants in the highest quintile of gPVG showed a 22.7% lower urinary Co (95% confidence interval (CI): −38.7; −1.98) and a 12.6% lower Se (95%CI: −22.9; −1.00) concentrations. Second quintile of adherence to hPVG was associated with a 51.7% lower urinary iAs + MMA concentrations (95%CI: −74.3; −8.61). Second quintile of adherence to an uPVG was associated with a 13.6% lower Se levels (95%CI: −22.9; −2.95) while the third quintile to this pattern was associated with 17.5% lower Mo concentrations (95%CI: −29.5; −2.95). The fourth quintile of adherence to gPVG was associated with a 68.5% higher PMI and a 53.7% lower SMI. Our study showed that adherence to a gPVG dietary pattern in childhood may modestly reduce the intakes of some essential metals such as Co and Se. Further investigations are warranted to explore any potential health implications. [ABSTRACT FROM AUTHOR]

STC-1 is a heterogeneous plurihormonal cell line producing several prominent gut peptide hormones. pGIP/Neo is a genetically selected sub-clone of STC-1 with augmented levels of glucose-dependent insulinotropic peptide (GIP). Morphometric parameters, hormone concentrations, mRNA transcripts, hormone immunocytochemistry and nutrient utilisation/production of these two cell lines were compared. Proglucagon-derived peptides (Glucagon-like peptide-1 (GLP-1) and – 2(GLP-2)) were lower in sub-clone cells than progenitor cells. High Content Analysis found altered intracellular GLP-1, GIP, cholecystokinin (CCK) and peptide YY (PYY) levels and differing hormone co-localisation. The proportion pGIP/Neo cells containing GIP immunoreactivity (82%) was greater than STC-1 (65%), as were the proportion with ‘GIP only’, ‘GLP − 1 + GIP’ or ‘GIP + PYY’ immunoreactivity. Most surprisingly mRNA transcripts of the proglucagon and GIP genes were inversely correlated to the levels of their translated peptides. This strongly suggests that proglucagon and GIP are encoded on ‘translationally regulated genes’ – a characteristic possessed by other endocrine hormones. Metabolomic profiling revealed differences in cellular nutrient utilisation/production and that under normal culture conditions both cell lines exhibit signs of overflow metabolism. These studies provide an insight into the metabolism and properties of these valuable cells, suggesting for the first time that incretin hormone genes are translationally regulated. [ABSTRACT FROM AUTHOR]

Runting-stunting syndrome (RSS) in broiler chickens is an enteric disease that causes significant economic losses to poultry producers worldwide due to elevated feed conversion ratios, decreased body weight during growth, and excessive culling. Of specific interest are the viral agents associated with RSS which have been difficult to fully characterize to date. Past research into the aetiology of RSS has implicated a wide variety of RNA and DNA viruses however, to date, no individual virus has been identified as the main agent of RSS and the current opinion is that it may be caused by a community of viruses, collectively known as the virome. This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Analysis of the viromes identified a total of 20 DNA and RNA viral families, along with 2 unidentified categories, comprised of 31 distinct viral genera and 7 unclassified genera. The most abundant viral families identified in this study were theAstroviridae,Caliciviridae,Picornaviridae,Parvoviridae,Coronaviridae,Siphoviridae, andMyoviridae.This study has identified historically significant viruses associated with the disease such as chicken astrovirus, avian nephritis virus, chicken parvovirus, and chicken calicivirus along with relatively novel viruses such as chicken megrivirus and sicinivirus 1 and will help expand the knowledge related to enteric disease in broiler chickens, provide insights into the viral constituents of a healthy avian gut, and identify a variety of enteric viruses and viral communities appropriate for further study. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa) cultivar Azucena—belonging to the Japonica subspecies—exudes high strigolactone (SL) levels and induces high germination of the root parasitic plant Striga hermonthica. Consistent with the fact that SLs also inhibit shoot branching, Azucena is a lowtillering variety. In contrast, Bala, an Indica cultivar, is a low-SL producer, stimulates less Striga germination, and is highly tillered. Using a Bala × Azucena F6 population, a major quantitative trait loci— qSLB1.1—for the exudation of SL, tillering, and induction of Striga germination was detected on chromosome 1. Sequence analysis of the corresponding locus revealed a rearrangement of a 51- to 59-kbp stretch between 28.9 and 29 Mbp in the Bala genome, resulting in the deletion of two cytochrome P450 genes—SLB1 and SLB2—with high homology to the Arabidopsis SL biosynthesis gene, MAX1. Both rice genes rescue the Arabidopsis max1-1 highly branched mutant phenotype and increase the production of the SL, ent-2′-epi-5-deoxystrigol, when overexpressed in Bala. Furthermore, analysis of this region in 367 cultivars of the publicly available Rice Diversity Panel population shows that the rearrangement at this locus is a recurrent natural trait associated with the Indica/Japonica divide in rice. [ABSTRACT FROM AUTHOR]

Biogenesis of mammalian mitochondrial ribosomes requires a concerted maturation of both the small (SSU) and large subunit (LSU). We demonstrate here that the m5C methyltransferase NSUN4, which forms a complex with MTERF4, is essential in mitochondrial ribosomal biogenesis as mitochondrial translation is abolished in conditional Nsun4 mouse knockouts. Deep sequencing of bisulfite-treated RNA shows that NSUN4 methylates cytosine 911 in 12S rRNA (m5C911) of the SSU. Surprisingly, NSUN4 does not need MTERF4 to generate this modification. Instead, the NSUN4/MTERF4 complex is required to assemble the SSU and LSU to form a monosome. NSUN4 is thus a dual function protein, which on the one hand is needed for 12S rRNA methylation and, on the other hand interacts with MTERF4 to facilitate monosome assembly. The presented data suggest that NSUN4 has a key role in controlling a final step in ribosome biogenesis to ensure that only the mature SSU and LSU are assembled. [ABSTRACT FROM AUTHOR]

Berlin high (BEH) and Berlin low (BEL) strains selected for divergent growth differ threefold in body weight. We aimed at examining muscle mass, which is a major contributor to body weight, by exploring morphological characteristics of the soleus muscle (fiber number and cross sectional area; CSA), by analyzing the transcriptome of the gastrocnemius and by initiating quantitative trait locus (QTL) mapping. BEH muscles were four to eight times larger than those of BEL. In substrain BEH+/+, mutant myostatin was replaced with a wild-type allele; however, BEH+/+muscles still were two to four times larger compared with BEL. BEH soleus muscle fibers were two times more numerous (P < 0.0001) and CSA was two times larger (P < 0.0001) compared with BEL. In addition, soleus femoral attachment anomaly (SFAA) was observed in all BEL mice. One significant (Chr 1) and four suggestive (Chr 3, 4, 6, and 9) muscle weight QTLs were mapped in a 21-day-old F2 intercross (n = 296) between BEH and BEL strains. The frequency of SFAA incidence in the F2 and in the backcross to BEL strain (BCI) suggested the presence of more than one causative gene. Two suggestive SFAA QTLs were mapped in BCL; however, their peak markers were not associated with the phenotype in F2. RNA-Seq analysis revealed 2,148 differentially expressed (P < 0.1) genes and 45,673 single nucleotide polymorphisms and >2,000 indels between BEH+/+and BEL males. In conclusion, contrasting muscle traits and genomic and gene expression differences between BEH and BEL strains provide a promising model for the search for genes involved in muscle growth and musculoskeletal morphogenesis. [ABSTRACT FROM AUTHOR]

Dietary restriction (DR) extends lifespan in a wide variety of species, yet the underlying mechanisms are not well understood. Here we show that the Caenorhabditis elegans HNF4α-related nuclear hormone receptor NHR-62 is required for metabolic and physiologic responses associated with DR-induced longevity. nhr-62 mediates the longevity of eat-2 mutants, a genetic mimetic of dietary restriction, and blunts the longevity response of DR induced by bacterial food dilution at low nutrient levels. Metabolic changes associated with DR, including decreased Oil Red O staining, decreased triglyceride levels, and increased autophagy are partly reversed by mutation of nhr-62. Additionally, the DR fatty acid profile is altered in nhr-62 mutants. Expression profiles reveal that several hundred genes induced by DR depend on the activity of NHR-62, including a putative lipase required for the DR response. This study provides critical evidence of nuclear hormone receptor regulation of the DR longevity response, suggesting hormonal and metabolic control of life span. [ABSTRACT FROM AUTHOR]

• DOM characteristics influence As methylation and biovolatilization in paddy soils. • Arsine production is markedly enhanced following pig manure DOM application. • Among DOMs, Pig manure DOM addition yields much higher As-methylation in paddy soil. • Pig manure DOM addition increases the OTU number of arsM -carrying bacteria. • High labile C amount is responsible for the enhanced As-methylation in paddy soils. The effect of dissolved organic matter (DOM), derived from composted pig manure or rice straw, on arsenic methylation and subsequent biovolatilization in paddy soils was investigated. Arsine production following pig manure DOM application was 2.7- and 9.6-fold higher than that of soils treated with rice straw DOM and the control, respectively. Trimethylarsine was the dominant arsine at 54 %, followed by dimethylarsine at 22 %, arsine at 21 %, and monomethylarsine at 3 %. The copy numbers of the total and As-methylating bacteria were significantly enhanced in paddy soils treated with DOM. Pig manure DOM altered soil bacterial profile by increasing the OTU number of As methylation-inducing bacteria, such as Proteobacteria, Bacteroidetes, Geobacter , Sphingomonas , Streptomyces , and Rhodopseudomonas , thereby promoting As volatilization and methylation in paddy soils. The higher relative content of alkyl-C, N-alkyl C, and carboxyl-C in pig manure DOM was responsible for the increase in total and arsM -carrying bacteria in paddy soils, leading to enhanced As methylation. These observations will promote a better understanding of the role of DOM in mediating As methylation and volatilization, along with how organic fertilization affects straighthead disorder of rice, a condition caused by methylated arsenic species. [ABSTRACT FROM AUTHOR]