Toposequential effects on water balance and productivity in rainfed lowland rice ecosystem in Southern Laos

In the Mekong region, most paddies in rainfed lowland rice (Oryza sativa L.) lie in a sequence on gentle sloping land, and grain yield (GY) often depends on the toposequence position. There is, however, lack of information on toposequential effects on field water supply in rainfed lowland rice and how that influences GY. A total of eight field experiments were carried out on sandy, coarse-textured soils in Southern Laos (Champassak Province and Savannakhet Province) over three wet seasons (2000-2002). Components of the water balance, including downward and lateral water movement (D and L, respectively), were quantified at three different positions along toposequences (top, middle and bottom). GY, days-to-flower (DTF) and rainfall were measured, and the water productivity (WP) was determined. In most experiments, standing water disappeared first in the top position and gradually in lower positions. This was associated with the observation that when there was standing water in the field, the higher position had larger D in both the provinces and also larger L in Champassak Province. However, in one experiment, water loss appeared later in the higher position, as the result of lower L, apparently due to some water inputs other than rainfall occurring at this position. Despite larger D plus L at the top position, seasonal sum of D and L were not much affected by the toposequence position, as the daily rate of D plus L became minimal when the standing water was lost earlier in the top position. Lower GY was associated with earlier disappearance of standing water from the field. Relatively low GY was expected in the top toposequence position. This was clearly shown in the toposequence of Phonthong, Champassak Province, as the timing of standing water disappearance relative to flowering was earlier in the top position. Variation in GY across the toposequence positions was coupled with the WP variation, and both GY and WP tended to decline with increased DTF. Therefore, variation in productivity of rainfed lowland rice across toposequence positions depends mainly on the field water status around flowering time. (c) 2005 Elsevier B.V. All rights reserved.

Fumonisina B1 em arroz: validação de método e efeito de tratamento térmico nos níveis da micotoxina

O arroz (Oryza sativa, L.), como todos os cereais, pode ser contaminado por fungos responsáveis por danos tecnol��gicos, nutricionais e toxicol��gicos, dentre eles a produção de micotoxinas. Diversas toxinas fúngicas produzidas pelo gênero Fusarium tem sido relatadas em arroz, no entanto a fumonisina B1 (FB1) é pouco estudada neste grão. As principais características da FB1 é a alta solubilidade em solventes polares, estabilidade a altas temperaturas al��m de efeitos neurotóxicos e carcinogênicos. Assim o objetivo deste trabalho foi avaliar o efeito do tratamento térmico e hidrotérmico nos teores de fumonisina B1 e nas características químicas de arroz comercial. Na primeira etapa do trabalho foi adaptado um método para detecção e quantificação de FB1 em arroz cru e após cocção, por HPLC-FL. O método foi avaliado quanto aos indicativos de eficiência destacando-se o LOD (30 µg.kg-1) e a recuperação ( 90% para arroz cru e 86% pra arroz cozido). Na segunda etapa realizou-se o levantamento de ocorrência de FB1 em 05 diferentes amostras comerciais de arroz integral, branco e parboilizado da cidade de Rio Grande, RS, totalizando 9 amostras. Foi detectada a presença de FB1 em 7 das 9 amostras, sendo que os maiores índices foram encontrados em amostras de arroz parboilizado e integral apresentando níveis de contaminação entre 30 e 170 µg.kg-1. A terceira etapa do trabalho consistiu no estudo do efeito de tratamentos térmicos sobre os níveis de FB1 em amostras após aplicação de calor. Foram testados tratamento hidrotérmico com evaporação, tratamento hidrotérmico com autoclavagem e tratamento térmico seco. O maior nível de redução dos teores iniciais de FB1 foi 82,8% quando se empregou tratamento térmico seco a 125 °C/3 min. Ainda foram avaliados os efeitos do t ratamento hidrotérmico com evaporação de água na composição química e na digestibilidade protéica. Esta característica proporcionou aumento de até 100% na digestibilidade in vitro das proteínas e reduziu em média 73% do teor de contaminação com FB1.

GGE biplot analysis of multi-environment yield trials of rice produced in a temperate climate

Low temperature is one of the main environmental constraints for rice ( Oryza sativa L.) grain production yield. It is known that multi-environment studies play a critical role in the sustainability of rice production across diverse environments. However, there are few studies based on multi-environment studies of rice in temperate climates. The aim was to study the performance of rice plants in cold environments. Four experimental lines and six cultivars were evaluated at three locations during three seasons. The grain yield data were analyzed with ANOVA, mixed models based on the best linear unbiased predictors (BLUPs), and genotype plus Genotype × Environment interaction (GGE) biplot. High genotype contribution (> 25%) was observed in grain yield and the interaction between genotype and locations was not very important. Results also showed that ‘Quila 241319’ was the best experimental line with the highest grain yield (11.3 t ha-1) and grain yield stability across the environments; commercial cultivars were classified as medium grain yield genotypes.

Cadmium availability and accumulation by lettuce and rice

Among the toxic elements, Cd has received considerable attention in view of its association with a number of human health problems. The objectives of this study were to evaluate the Cd availability and accumulation in soil, transfer rate and toxicity in lettuce and rice plants grown in a Cd-contaminated Typic Hapludox. Two simultaneous greenhouse experiments with lettuce and rice test plants were conducted in a randomized complete block design with four replications. The treatments consisted of four Cd rates (CdCl2), 0.0; 1.3; 3.0 and 6.0 mg kg(-1), based on the guidelines recommended by the Environmental Agency of the State of São Paulo, Brazil (Cetesb). Higher Cd rates increased extractable Cd (using Mehlich-3, Mehlich-1 and DTPA chemical extractants) and decreased lettuce and rice dry matter yields. However, no visual toxicity symptoms were observed in plants. Mehlich-1, Mehlich-3 and DTPA extractants were effective in predicting soil Cd availability as well as the Cd concentration and accumulation in plant parts. Cadmium concentration in rice remained below the threshold for human consumption established by Brazilian legislation. on the other hand, lettuce Cd concentration in edible parts exceeded the acceptable limit.

Utilization of nitrogen (15N) from urea and green manures by rice as affected by nitrogen fertilizer rate.

The use of green manures (GMs) in combination with nitrogen (N) fertilizer application is a promising practice to improve N fertilizer management in agricultural production systems. The main objective of this study was to evaluate the N use efficiency (NUE) of rice plant, derived from GMs including sunn hemp (Crotalaria juncea L.), millet (Pennisetum glaucum L.) and urea in the greenhouse. The experimental treatments included two GMs (sunn hemp-15N and millet-15N), absence of N organic source (without GM residues in soil) and four N rates, as urea-15N (0, 28.6, 57.2 and 85.8 mg N kg-1). The results showed that both rice grain and straw biomass yields under sunn hemp were greater than that of millet or without the application of GM. The NUE of rice under sunn hemp was greater than that under millet (18.9 and 7.8% under sunn hemp and millet, respectively). The urea N application rates did not affect the fertilizer NUE by rice (53.7%) with or without GMs. The NUE of GMs by rice plants ranged from 14.1% and 16.8% for root and shoot, respectively. The study showed that green manures can play an important role in enhancing soil fertility and N supply to subsequent crops.

Soil management, seed treatment and soil compaction on the sowing furrows affect grain yields of upland rice genotypes.

The water availability for flood irrigated rice (Oryza sativa L.) is decreasing worldwide. Therefore, developing technologies to allow growing rice in aerobic condition, such as a no-tillage system (NTS) can contribute to produce upland rice grains without yield losses and also in saving more water. The objective of this study was to determine the effect of soil management, seed treatment and compaction on the sowing furrow on grain yield of upland rice genotypes. We made two trials, one in an NTS and another using conventional tillage, CT (one plowing and two diskings). The field experiments were performed in the Central Region of Brazil in Cerrado soils. For each trial, the experimental design was a randomized block design in a factorial scheme, with three replications. The treatments consisted of a combination of 10 genotypes with 2 compaction pressures on the sowing furrow (25 kPa and 126kPa) and 2 types of seed treatment (with and without pesticide). Under CT, the seed treatment did not contribute to increase upland rice grain yields. However, under NTS the grain yield of some genotypes [BRS Esmeralda (from 723 to 1,766 kg ha-1), BRS Pepita (from 930 to 1,874 kg ha-1), AB072044 (from 523 to 1,579 kg ha-1), and AB072085 (from 632 to 1,636 kg ha-1) at 25 kPA soil compaction pressure, and Sertaneja (from 994 to 2,167 kg ha-1), BRS Pepita (from 1,161 to 2,100 kg ha-1), and AB072085 (from 958 to 2,213 kg ha-1), at 126 kPA soil compaction pressure] increased with the use of this practice. At CT the higher soil compaction pressure on the sowing furrow (from 25 kPa to 126 kPa) increased rice grain yield only when it was used seed treatment and the genotypes Serra Dourada (from 1,239 to 2,178 kg ha-1), Sertaneja (from 1,510 to 2,379 kg ha-1), and Cambará (from 1,877 to 2,831 kg ha-1). On the other hand, under NTS, increasing soil compaction pressure on the sowing furrow allowed for an increased rice grain yield of Serra Dourada (from 1,553 to 2,347 kg ha-1), Esmeralda (from 723 to 1,643 kg ha-1), AB072044 (from 523 to 2,040 kg ha-1), and Cambará (from 1,243 to 2,032 kg ha-1) without seed treatment and Sertaneja (from 1,385 to 2,167 kg ha-1) and AB072044 (from 1,579 to 2,356 kg ha-1) with seed treatment. In CT the most productive genotypes were AB062008 (2,714 kg ha-1) and BRSMG Caravera (2,479 kg ha-1), while at NTS were the genotypes: BRSGO Serra Dourada (2,118 kg ha-1), AB072047 (1,888 kg ha-1), AB062008 (1,823 kg ha-1), BRSMG Caravera (1,737 kg ha-1), Cambará (1,716 kg ha-1), AB072044 (1,625 kg ha-1), BRS Esmeralda (1,604 kg ha-1), and BRS Pepita (1,516 kg ha-1).

High-yeld RNA-extraction method for saliva

BACKGROUND: The use of salivary diagnostics is increasing because of its noninvasiveness, ease of sampling, and the relatively low risk of contracting infectious organisms. Saliva has been used as a biological fluid to identify and validate RNA targets in head and neck cancer patients. The goal of this study was to develop a robust, easy, and cost-effective method for isolating high yields of total RNA from saliva for downstream expression studies. METHODS: Oral whole saliva (200 mu L) was collected from healthy controls (n = 6) and from patients with head and neck cancer (n = 8). The method developed in-house used QIAzol lysis reagent (Qiagen) to extract RNA from saliva (both cell-free supernatants and cell pellets), followed by isopropyl alcohol precipitation, cDNA synthesis, and real-time PCR analyses for the genes encoding beta-actin ("housekeeping" gene) and histatin (a salivary gland-specific gene). RESULTS: The in-house QIAzol lysis reagent produced a high yield of total RNA (0.89 -7.1 mu g) from saliva (cell-free saliva and cell pellet) after DNase treatment. The ratio of the absorbance measured at 260 nm to that at 280 nm ranged from 1.6 to 1.9. The commercial kit produced a 10-fold lower RNA yield. Using our method with the QIAzol lysis reagent, we were also able to isolate RNA from archived saliva samples that had been stored without RNase inhibitors at -80 degrees C for >2 years. CONCLUSIONS: Our in-house QIAzol method is robust, is simple, provides RNA at high yields, and can be implemented to allow saliva transcriptomic studies to be translated into a clinical setting.

Saliva proteome research: current status and future outlook

Human saliva harbours proteins of clinical relevance and about 30% of blood proteins are also present in saliva. This highlights that saliva can be used for clinical applications just as urine or blood. However, the translation of salivary biomarker discoveries into clinical settings is hampered by the dynamics and complexity of the salivary proteome. This review focuses on the current status of technological developments and achievements relating to approaches for unravelling the human salivary proteome. We discuss the dynamics of the salivary proteome, as well as the importance of sample preparation and processing techniques and their influence on downstream protein applications; post-translational modifications of salivary proteome and protein: protein interactions. In addition, we describe possible enrichment strategies for discerning post-translational modifications of salivary proteins, the potential utility of selected-reaction-monitoring techniques for biomarker discovery and validation, limitations to proteomics and the biomarker challenge and future perspectives. In summary, we provide recommendations for practical saliva sampling, processing and storage conditions to increase the quality of future studies in an emerging field of saliva clinical proteomics. We propose that the advent of technologies allowing sensitive and high throughput proteome-wide analyses, coupled to well-controlled study design, will allow saliva to enter clinical practice as an alternative to blood-based methods due to its simplistic nature of sampling, non-invasiveness, easy of collection and multiple collections by untrained professionals and cost-effective advantages.

A novel saliva-based microRNA biomarker panel to detect head and neck cancers

Background MicroRNAs (miRNAs) are known to play an important role in cancer development by post-transcriptionally affecting the expression of critical genes. The aims of this study were two-fold: (i) to develop a robust method to isolate miRNAs from small volumes of saliva and (ii) to develop a panel of saliva-based diagnostic biomarkers for the detection of head and neck squamous cell carcinoma (HNSCC). Methods Five differentially expressed miRNAs were selected from miScript™ miRNA microarray data generated using saliva from five HNSCC patients and five healthy controls. Their differential expression was subsequently confirmed by RT-qPCR using saliva samples from healthy controls (n = 56) and HNSCC patients (n = 56). These samples were divided into two different cohorts, i.e., a first confirmatory cohort (n = 21) and a second independent validation cohort (n = 35), to narrow down the miRNA diagnostic panel to three miRNAs: miR-9, miR-134 and miR-191. This diagnostic panel was independently validated using HNSCC miRNA expression data from The Cancer Genome Atlas (TCGA), encompassing 334 tumours and 39 adjacent normal tissues. Receiver operating characteristic (ROC) curve analysis was performed to assess the diagnostic capacity of the panel. Results On average 60 ng/μL miRNA was isolated from 200 μL of saliva. Overall a good correlation was observed between the microarray data and the RT-qPCR data. We found that miR-9 (P <0.0001), miR-134 (P <0.0001) and miR-191 (P <0.001) were differentially expressed between saliva from HNSCC patients and healthy controls, and that these miRNAs provided a good discriminative capacity with area under the curve (AUC) values of 0.85 (P <0.0001), 0.74 (P < 0.001) and 0.98 (P < 0.0001), respectively. In addition, we found that the salivary miRNA data showed a good correlation with the TCGA miRNA data, thereby providing an independent validation. Conclusions We show that we have developed a reliable method to isolate miRNAs from small volumes of saliva, and that the saliva-derived miRNAs miR-9, miR-134 and miR-191 may serve as novel biomarkers to reliably detect HNSCC. © 2014 International Society for Cellular Oncology.

Breastmilk-saliva interactions boost innate immunity by regulating the oral microbiome in early infancy

Introduction Xanthine oxidase (XO) is distributed in mammals largely in the liver and small intestine, but also is highly active in milk where it generates hydrogen peroxide (H2O2). Adult human saliva is low in hypoxanthine and xanthine, the substrates of XO, and high in the lactoperoxidase substrate thiocyanate, but saliva of neonates has not been examined. Results Median concentrations of hypoxanthine and xanthine in neonatal saliva (27 and 19 μM respectively) were ten-fold higher than in adult saliva (2.1 and 1.7 μM). Fresh breastmilk contained 27.3±12.2 μM H2O2 but mixing baby saliva with breastmilk additionally generated >40 μM H2O2, sufficient to inhibit growth of the opportunistic pathogens Staphylococcus aureus and Salmonella spp. Oral peroxidase activity in neonatal saliva was variable but low (median 7 U/L, range 2–449) compared to adults (620 U/L, 48–1348), while peroxidase substrate thiocyanate in neonatal saliva was surprisingly high. Baby but not adult saliva also contained nucleosides and nucleobases that encouraged growth of the commensal bacteria Lactobacillus, but inhibited opportunistic pathogens; these nucleosides/bases may also promote growth of immature gut cells. Transition from neonatal to adult saliva pattern occurred during the weaning period. A survey of saliva from domesticated mammals revealed wide variation in nucleoside/base patterns. Discussion and Conclusion During breast-feeding, baby saliva reacts with breastmilk to produce reactive oxygen species, while simultaneously providing growth-promoting nucleotide precursors. Milk thus plays more than a simply nutritional role in mammals, interacting with infant saliva to produce a potent combination of stimulatory and inhibitory metabolites that regulate early oral���and hence gut–microbiota. Consequently, milk-saliva mixing appears to represent unique biochemical synergism which boosts early innate immunity.

Enrichment and identification of glycoproteins in human saliva using lectin magnetic bead arrays

Aberrant glycosylation of proteins is a hallmark of tumorigenesis, and could provide diagnostic value in cancer detection. Human saliva is an ideal source of glycoproteins due to the relatively high proportion of glycosylated proteins in the salivary proteome. Moreover, saliva collection is non-invasive, technically straightforward and the sample collection and storage is relatively easy. Although, differential glycosylation of proteins can be indicative of disease states, identification of differential glycosylation from clinical samples is not trivial. To facilitate salivary glycoprotein biomarker discovery, we optimised a method for differential glycoprotein enrichment from human saliva based on lectin magnetic bead arrays (saLeMBA). Selected lectins from distinct reactivity groups were used in the saLeMBA platform to enrich salivary glycoproteins from healthy volunteer saliva. The technical reproducibility of saLeMBA was analysed with LC-MS/MS to identify the glycosylated proteins enriched by each lectin. Our saLeMBA platform enabled robust glycoprotein enrichment in a glycoprotein- and lectin-specific manner consistent with known protein-specific glycan profiles. We demonstrated that saLeMBA is a reliable method to enrich and detect glycoproteins present in human saliva.

稻属Oryza officinalis复合体基因组研究－兼论基因组原位杂交的原理和方法

稻属（Oryza L.）属于禾本科稻族（Oryzeae Dumortier）。本属包括AA，BB，BBCC，CC，CCDD，EE，FF，GG，HHJJ和HHKK十个基因组，二十余种。其中Oryza officinalis复合体包括BB，BBCC，CC，CCDD和EE五个基因组，九个种。众多的学者对该复合体进行了广泛深入的研究，为后续研究奠定了坚实的基础。然而，迄今为止，多倍体物种形成问题许多没有解决，基因组间的关系尚未完全阐明，甚至有些多倍体物种的基因组组成仍未确认。 本文评述了Oryza officinalis复合体中基因组研究的历史和现状，用基因组原位杂位（GISH）的方法，对该复合体四倍体物种的基因组组成作了验证;对B，C，D和E四个基因组间的关系进行了研究。同时对基因组原位杂交的方法，原位杂交鉴定多倍体基因组的组成以及研究基因组间关系的方法作了一些探讨。其主要研究结果如下： 一. 原杂交方法的研究：1）染色体制片：比较研究了不同的制片方法，发现压片法适用于大染色体的材料;将酶解/空气干燥法（Fukui et al., 1992）加以改进后，特别适宜于小染色体植物材料的制片。2）根尖储存时间和条件对原位杂交的影响：发现在-20 ℃的酒精（70%）中储存8个月以内的根尖材料，可用于原位杂交;而在-20 ℃的固定液中储藏18个月的根尖，DNA降解严重，不能用于GISH。3）探针标记：比较了随机引物法、缺口平移法和两步标记法（先用随机引物标记后，再用缺口平移法进行标记的方法）的优缺点。结果显示两步标记法是最佳标记方法。 二. GISH鉴定异源多倍体的方法：用两个异源四倍体Oryza minuta和Scilla sinensis (2n = 34)做染色体制片，进行原位杂交实验，结果表明：1）用二倍体亲本基因组之一做探针而不用封阻DNA， 可以鉴别Oryza minuta而不能鉴别Scilla sinensis中的基因组。2）用一个二倍体亲本做探针而用另一个做封阻，能够区分Scilla sinensis的两个基因组;但过量的封阻DNA将可以造成一些实验假象。3）同时用两个亲本的DNA做探针，不仅能够有效分辨不同的基因组，还能够根据交叉杂交程度推测基因组间的分化程度，是鉴别异源多倍体最有效的方法。 三. GISH鉴定稻属四倍体的基因组组成：1）Oryza minuta, O. punctata和O. malampuzhaensis的基因组的组成都为BBCC。2）Oryza minuta中B基因组和二倍体O. punctata中的B基因组之间存在着明显的基因组内分化。3）O. alta是一个异源多倍体，其基因组组成为CCDD。但C和D之间的分化不彻底，可以认为它不是一个严格意义上的异源多倍体。 四. GISH研究B，C，D和E基因组间的关系：1）B基因组和C基因组之间的关系最远;E和C之间的分化同E和B之间的分化程度接近，但E和C之间的分化比E和D之间的分化要小一些;C和D之间的分化不彻底，关系最近。

The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Responses of Artemisia frigida Willd. (Compositae) and Leymus chinensis (Trin.) Tzvel. (Poaceae) to sheep saliva

Although studies show that grazing and browsing by herbivores have marked effects on host plants, the mechanisms remain unclear. The objective of this study is to determine the effects of sheep saliva on host plant growth. Sheep saliva was manually applied to clipped plants of two different life forms, a semi-shrub, Artemisia frigida Willd., and a herbaceous species, Leymus chinensis (Trin.) Tzevel. The results showed that sheep saliva significantly enhanced aboveground net primary productivity (ANPP) and the ratio of ANPP to belowground net primary productivity (BNPP) for both species. This indicated that sheep saliva promotes aboveground compensatory growth and allocation of photosynthate to aboveground for both plant species. Sheep saliva stimulated only tillering of L. chinensis. Regardless of saliva application, clipping significantly decreased BNPP and plant height, but significantly increased the number of branches or tillers for both plant species. The relative growth rates (RGRs) on both species were significantly greater after clipping with saliva compared with control and clipping without saliva treatments. In addition, RGR of the herbaceous species L. chinensis was faster than that of the semi-shrub A. frigida after application of saliva. (c) 2006 Elsevier Ltd. All rights reserved.