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This study was carried out to determine the impacts co-compost of Pleurotus geesteranus spent mushroom substrate and chicken manure (SMC) on seedling quality, rhizosphere microbial characteristics, as well as fungal pathogens in rice seedling substrates. Results showed that incorporating SMC within the substrate, especially 50% volume (R2), increased rice seedling growth and vitality without external fertilization at the seedling growth stage. Moreover, SMC amendment increased microbial activity, and promoted rice seedling recruitment of plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF), and significantly reduced the abundance of pathogenic fungi, especially Magnaporthe grisea, and thus reducing soil-borne diseases. It is conducive to the sustainable development of cultivated land and agricultural waste recycling.

Increasing both carbon (C) sequestration and food production is essential for a sustainable future. However, increasing soil C sequestration or graining yield/quality in rice (Oryza sativa L.) systems has been a tradeoff in that pursuing one goal may compromise the other goal. Field experiments were designed to evaluate methane emission and grain yield in two rice systems in southern China, including the traditional double rice with a seedling transplanting system and innovative ratoon rice with a direct seeding system. Grain yield, grain quality, methane (CH

This study analyzed the effects of traditional rice cultivation (TC), ridge tillage and terrace rice cultivation (RC), and ridge tillage and terrace rice cultivation plus loach (Misgurnus anguillicaudatus) breeding in ditches (RLC) on methane (CH4) emissions and daytime net ecosystem production (NEP) of CO2 fluxes in a paddy ecosystem using the ultra-portable greenhouse gas (GHG) analyzer with a static transparent chamber. Rice plant characteristics and yields were also measured with field experiments and laboratory analysis. The aim was to explore the possible contribution of the rice ridge terraced cultivation to yield while reducing GHG emissions. We found that (1) RC has the highest rice yield for both the early-and late-season rice, followed by TC and RLC. (2) The combined CH4 emission and daytime NEP values were the least for RC during the double growing season, followed by TC and RLC. (3) Comparing the cumulative global warming potential and yield-scaled emission, RC showed the lowest GHG emission and the highest NEP for the double growing season, followed by TC and RLC. The results indicated that RC was beneficial for increasing rice yields while decreasing CO2 and CH4 emissions in the paddy ecosystem.

Ecological rice-cropping systems (ERSs) are prosperous rice ecosystems that have a profound influence on global greenhouse (GHG) effects. However, the high variation in research results requires an accurate evaluation of the ERS effects. In this study, three typical ERS modes, rice-crayfish, rice-duck, and rice-fish were selected, and a meta-analysis was conducted using the data of 34 studies to comprehensively evaluate the effects of ERSs on GHG emissions, the global warming potential (GWP), and GHG intensity (GHGI). The results showed that the ERSs reduced CH4 emissions significantly (-12.5%), but increased N2O emissions by 11.3% as compared with traditional rice-cropping systems (TRSs). Further, ERSs have slightly lower GWP, rice yield, and GHGI values (6.5%, 5.5%, and 5.6%, respectively) than TRSs. The rice-crayfish and rice-duck modes significantly alleviated the GWP by 18.0% and 11.1%, respectively, whereas the rice-fish mode enhanced the GWP by 20.8%. Moreover, the rice-duck mode significantly reduced the GHGI by 17.2%, while the ricecrayfish and rice-fish modes increased the GHGI by 9.7% and 8.8%, respectively. Further, the ERSs significantly changed the dissolved oxygen concentration in the flood water as well as the Eh, dissolved organic carbon, and ammonium nitrogen in the soil, wherein the effect sizes of the ERSs on the GHG emissions were significantly correlated with their respective increase. Considering the net ecosystem economic budget and CO2 emissions equivalent/output, ERSs were found to be effective "green technologies". Further, we found that the rice-duck ERS was a good ecological ricecropping system for global warming mitigation. Our study provided new ideas for sustainable agriculture.

Tea plants are important economic perennial crops that can be negatively impacted by drought stress (DS). However, their survival strategies in long-term DS conditions and the accumulation and influence of metabolites and mineral elements (MEs) in their organs, when facing hydraulic vulnerability segmentation, require further investigation. The MEs and metabolites in the leaf, stem, and root after long-term DS (20 d) were examined here, using inductively coupled plasma optical emission spectrometry (ICP-OES) and liquid chromatograph-mass spectrometry (LC-MS). The accumulation patterns of 116 differentially accumulated metabolites (DAMs) and nine MEs were considerably affected in all organs. The concentration of all MEs varied significantly in at least one organ, while the K and Ca levels were markedly altered in all three. Most DAM levels increased in the stem but decreased in the root and leaf, implying that vulnerability segmentation may occur with long-term DS. The typical nitrogen- and carbon-compound levels similarly increased in the stem and decreased in the leaf and root, as the plant might respond to long-term DS by stabilizing respiration, promoting nitrogen recycling, and free radical scavenging. Correlation analysis showed several possible DAM-ME interactions and an association between Mn and flavonoids. Thus, survival strategies under long-term DS included sacrificing distal/vulnerable organs and accumulating function-specialized metabolites and MEs to mitigate drought-induced oxidative damage. This is the first study that reports substance fluctuations after long-term DS in different organs of plants, and highlights the need to use whole plants to fully comprehend stress response strategies.

Using symbiotic farming methods [cover crops and chicken grazing (+ C)] in a winter fallow field, we found that the soil organic matter and total nitrogen of the + C treatment were 5.2% and 26.6% higher, respectively, than those of a treatment with cover crops and no chicken grazing (− C). The annual rice grain yield of the + C treatment was 3.8% higher than that of the − C treatment and 12.3% higher than that of the bare fallow field (CK), while the annual CH4 emissions of the + C treatment were 26.9% lower than those of the − C treatment and 10.6% lower than those of the CK treatment. The 100-year global warming potential of the + C treatment was 6.2% lower than that of the − C treatment. Therefore, the use of winter cover crops and chicken grazing in a winter fallow field was effective at reducing CH4 emissions and significantly improving soil nutrients and rice yield.

No-tillage (NT) management is considered a leading approach for sustaining crop production and improving soil and environmental quality. Based on a long-term no-tillage experiment in a rice–oilseed rape cropping system, we examined differences in soil organic matter (SOM), soil microbial carbon (C) and nitrogen (N) content, and CH4 and CO2 fluxes between NT and conventional tillage (CT) management. SOM under NT was 21.0 g kg–1, and a significant difference was detected between 2004 and 2014. SOM increased under NT and CT by averages of 0.60 and 0.32 g kg–1 year–1, respectively. Soil microbial C and N content were higher under CT than under NT. However, soil C:N ratios under NT were 17.4 and 9.7% higher than under CT, respectively, whereas soil microbial C:N ratios under NT were on average 9.47 and 9.7% higher. In addition, about 70% of CO2 net uptake and over 99% of net CH4 emissions occurred during the rice season in May–September in the rice–oilseed rape cropping system. Annual cumulative CH4 and daytime net ecosystem CO2 exchange (NEE) under NT was 1,813.9 g CO2 equiv. m–2, 10.8% higher than that under CT. Thus, our results suggest that a higher soil microbial C:N ratio and NEE (CH4 and daytime CO2) could contribute to increasing SOM/C in the surface soil under NT management.

Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence., Genome assembly for many plant species can be challenging due to large size and high repeat content. Here, the authors use in vitro proximity ligation to assemble the genome of lettuce, revealing a family-specific triplication event and providing a comprehensive reference genome for a member of the Compositae.

The ability to induce a defense response after pathogen attack is a critical feature of the immune system of any organism. Nucleotide-binding leucine-rich repeat receptors (NLRs) are key players in this process and perceive the occurrence of nonself-activities or foreign molecules. In plants, coevolution with a variety of pests and pathogens has resulted in repertoires of several hundred diverse NLRs in single individuals and many more in populations as a whole. However, the mechanism by which defense signaling is triggered by these NLRs in plants is poorly understood. Here, we show that upon pathogen perception, NLRs use their N-terminal domains to transactivate other receptors. Their N-terminal domains homo- and heterodimerize, suggesting that plant NLRs oligomerize upon activation, similar to the vertebrate NLRs; however, consistent with their large number in plants, the complexes are highly heterometric. Also, in contrast to metazoan NLRs, the N-terminus, rather than their centrally located nucleotide-binding (NB) domain, can mediate initial partner selection. The highly redundant network of NLR interactions in plants is proposed to provide resilience to perturbation by pathogens., Author summary The ability to induce defenses in response to pathogen attack is a critical feature of immunity in any organism. Nucleotide-binding leucine-rich repeat receptors (NLRs) are key players in this process and have evolved to perceive the occurrence of nonself-activities or foreign molecules. In plants, coevolution with a variety of pests and pathogens has resulted in repertoires of several hundred diverse NLRs in single individuals and many more in populations as a whole. The mechanism by which defense signaling is triggered by these NLRs is poorly understood. Here, we show that upon pathogen perception, NLRs use their N-terminal domains to transactivate other receptors. Their N-terminal domains homo- and heterodimerize, suggesting that plant NLRs oligomerize upon activation, similar to the vertebrate NLRs; however, consistent with their large number in plants, their complexes are highly heterometric. Also, in contrast to metazoan NLRs, their N-terminus, rather than their centrally located nucleotide-binding (NB) domain, can mediate initial partner selection. The highly redundant network of NLR interactions is proposed to provide resilience to perturbation by pathogens.

Some soil bacteria and fungi are known to solubilize phosphates and play an important role in supplying phosphorus (P) to plants. In this study, we characterized the phosphate-solubilizing bacteria and fungi as well as P availability in latosols from southern China under different land use practices. Three different latosols (i.e., red soil, lateritic red soil and laterite red soil), each with four different land uses (i.e., agricultural land, grass land, forest land and orchard land), from Guangdong Province, China, were chosen to determine the amounts of phosphate-solubilizing bacteria (PSB) and phosphate-solubilizing fungi (PSF) and their phosphate solubilizing abilities. Our results show that the amount of available P (AP) increased with the amount of PSB favored in solubilizing organic P (or PSBop), while the amount of PSF increased with the content of soil organic carbon (SOC). The average rates of phosphate solubilization were 28.23% for PSBop, 6.97% for PSF, and 0.16% for PSBip (PSB favored in solubilizing inorganic P). An increase in soil pH decreased the ability of PSB to solubilize phosphate in latosols. This ability occurred in the following order: PSBop > PSF > PSBip. No significant difference in the amount of PSF was observed among the four different land uses for the lateritic red soil and laterite red soil, whereas a profound significant difference was found for the red soil, with the highest number of PSF in the grass land. Reasonable linear correlations between the PSB and the AP and between the PSF and the SOC were obtained and could provide a good reference to characterize soil PSB and PSF. Additionally, PSBop was the best bacterial species to solubilize phosphate in the latosols.

Winter fallow is important for renewing and improving soil fertility under double-cropping rice systems, such as those in southern China. Using a regenerative farming technology of integrating grass-chicken farming in a winter fallow field, we investigated soil nitrogen conversion and assessed the agricultural economic benefits of the whole farmland ecosystem. To test the effects of chicken grazing on the fallow system, we established field treatments involving adding chickens to a field planted with the cover crops, including cover milk vetch (Astragalus sinicus) with chicken grazing treatment (MC) and cover ryegrass (Lolium spp.) with chicken grazing (RC); cover crops only, including cover milk vetch (Astragalus sinicus) treatment (M) and cover ryegrass (Lolium spp.) (R); and a bare fallow field treatment (CK). We found that both cover crops (M and R) and cover crops with chicken grazing (MC and RC) increased nitrate, ammonium, dissolved organic nitrogen, and total nitrogen contents, and the increase was higher in MC and RC treatments. We also observed increased straw biomass and grain yield in the all four treatments, with more increases with chicken treatments as compared with CK. On the economic profits, MC increased by 101.72% and RC increased by 104.12% as compared with CK, while R increased by 5.19% and M reduced by 1.86% as compared with CK. The nitrogen transfer rate (the output/input ratio) of MC, RC, M, and R increased by 66.71%, 71.50%, 65.97%, and 59.97%, respectively, while the nitrogen accumulation rate (input-output) of MC, RC, M, and R increased by 480.56%, 612.98%, 356.74%, and 267.65%, respectively. Our study demonstrates that retaining nitrogen and gaining economic profit by integrating cover crops with chicken grazing is potentially more sustainable than adding cover crops alone. We further suggest that using the integrated grass-livestock farming technology can reduce environmental damage caused by commercial fertilizers.

Modifications of plant immune complexes by secreted pathogen effectors can trigger strong immune responses mediated by the action of nucleotide binding-leucine-rich repeat immune receptors. Although some strains of the pathogen Pseudomonas syringae harbor effectors that individually can trigger immunity, the plant’s response may be suppressed by other virulence factors. This work reveals a robust strategy for immune suppression mediated by HopZ3, an effector in the YopJ family of acetyltransferases. The suppressing HopZ3 effector binds to and can acetylate multiple members of the RPM1 immune complex, as well as two P. syringae effectors that together activate the RPM1 complex. These acetylations modify serine, threonine, lysine, and/or histidine residues in the targets. Through HopZ3-mediated acetylation, it is possible that the whole effector-immune complex is inactivated, leading to increased growth of the pathogen., Graphical abstract

A laboratory experiment was performed to examine the impact of simulated acid rain (SAR) on nutrient leaching, microbial biomass, and microbial activities in a lateritic red soil in South China. The soil column leaching experiment was conducted over a 60-day period with the following six SAR pH treatments (levels): 2.5, 3.0, 3.5, 4.0, 4.5, and 5.0 and one control treatment (pH = 7). Compared with the control treatment, the concentrations of soil organic matter, total nitrogen, total phosphorus, total potassium, soil microbial biomass carbon (MBC), soil microbial biomass nitrogen (MBN), and average well color density (AWCD) in the Ecoplates were all significantly decreased by leaching with SAR at different pH levels. The decrease in MBC and MBN indicated that acid rain reduced the soil microbial population, while the decrease in AWCD revealed that acid rain had a negative effect on soil bacterial metabolic function. Soil basal respiration increased gradually from pH 4.0 to 7.0 but decreased dramatically from pH 2.5 to 3.0. The decrease in soil nutrient was the major reason for the change of soil microbial functions. A principal component analysis showed that the major carbon sources used by the bacteria were carbohydrates and carboxylic acids.

Rice–duck farming is a sustainable food system that provides rice and duck meat and eggs. Excessive application of commercial feedstuff for ducks weakens the sustainability of rice–duck farming. This study aims to investigate green forage (Lolium multiflorum Lam.) as a substitute for commercial grain mix, to attain a maximum economic benefit and pollution-free production in rice–duck farming. The effects of a mixed feedstuff of green forage and commercial grain mix with a stable ratio of 1:4 (MFSR), mixture feedstuff of green forage and commercial grain mix with dynamic ratios (MFDR), and full commercial grain mix (FCGM) were studied. Results showed that Cherry Volley and hybrid ducks were more adaptable to mixed feedstuff than Mud ducks. Growth of ducks was classified into rapid, slow and steady-growth stages. The weight, body length, neck length, and chest circumference of ducks that were fed MFDR were only slightly decreased. The carcass weight, eviscerated weight, and semi-eviscerated weight of ducks ...

Acid rain is one of the most serious ecological and environmental problems worldwide. This study investigated the impacts of simulated acid rain (SAR) upon leaching of trace metals and aluminum (Al) from a soil. Soil pot leaching experiments were performed to investigate the impacts of SAR at five different pH levels (or treatments) over a 34-day period upon the release of trace metals (i.e., Cu, Ni, Pb, Zn, and Fe) and Al from the Latosol (acidic red soil). The concentrations of trace metals in the effluent increased as the SAR pH level decreased, and were highest at the SAR pH = 2.0. In general, the concentrations of Cu, Pb, Fe, and Al in the effluent increased with leaching time at the SAR pH = 2.0, whereas the concentrations of Zn, Fe, and Al in the effluent decreased with leaching time at the SAR pH ≥ 4.0. The increase in electrical conductivity (EC) with leaching time at five different SAR pH levels was primarily due to the concentrations of Al and Fe in the effluent. There were good linear correlat...

Excess aluminum (Al) in soils due to acid rain leaching is toxic to water resources and harmful to soil organisms and plants. This study investigated adverse impacts of Al levels upon earthworms (Eisenia fetida) from the latosol (acidic red soil). Laboratory experiments were performed to examine the survival and avoidance of earthworms from high Al concentrations and investigate the response of earthworms upon Al toxicity at seven different Al concentrations that ranged from 0 to 300 mg kg(-1) over a 28-day period. Our study showed that the rate of the earthworm survival was 100 % within the first 7 days and decreased as time elapsed, especially for the Al concentrations at 200 and 300 mg kg(-1). A very good linear correlation existed between the earthworm avoidance and the soil Al concentration. There was no Al toxicity to earthworms with the Al concentration ≤ 50 mg kg(-1), and the toxicity started with the Al concentration ≥ 100 mg kg(-1). Low Al concentration (i.e.,50 mg kg(-1)) enhanced the growth of the earthworms, while high Al concentration (100 mg kg(-1)) retarded the growth of the earthworms. The weight of earthworms and the uptake of Al by earthworms increased with the Al concentrations from 0 to 50 mg kg(-1) and decreased with the Al concentrations from 50 to 300 mg kg(-1). The protein content in the earthworms decreased with the Al concentrations from 0 to 100 mg kg(-1) and increased from 100 to 300 mg kg(-1). In contrast, the catalase (CAT) and superoxide dismutase (SOD) activities in the earthworms increased with the Al concentrations from 0 to 100 mg kg(-1) and decreased from 100 to 300 mg kg(-1). The highest CAT and SOD activities and lowest protein content were found at the Al concentration of 100 mg kg(-1). Results suggest that a high level of Al content in latosol was harmful to earthworms.

Bacterial plant pathogens manipulate their hosts by injection of numerous effector proteins into host cells via type III secretion systems. Recognition of these effectors by the host plant leads to the induction of a defense reaction that often culminates in a hypersensitive response manifested as cell death. Genes encoding effector proteins can be exchanged between different strains of bacteria via horizontal transfer, and often individual strains are capable of infecting multiple hosts. Host plant species express diverse repertoires of resistance proteins that mediate direct or indirect recognition of bacterial effectors. As a result, plants and their bacterial pathogens should be considered as two extensive coevolving groups rather than as individual host species coevolving with single pathovars. To dissect the complexity of this coevolution, we cloned 171 effector-encoding genes from several pathovars of Pseudomonas and Ralstonia. We used Agrobacterium tumefaciens-mediated transient assays to test the ability of each effector to induce a necrotic phenotype on 59 plant genotypes belonging to four plant families, including numerous diverse accessions of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum). Known defense-inducing effectors (avirulence factors) and their homologs commonly induced extensive necrosis in many different plant species. Nonhost species reacted to multiple effector proteins from an individual pathovar more frequently and more intensely than host species. Both homologous and sequence-unrelated effectors could elicit necrosis in a similar spectrum of plants, suggesting common effector targets or targeting of the same pathways in the plant cell.

The present study examined the influence of the different fertilization on the dynamic of soil microbial biomass carbon (SMBC) of red soil in tea gardens. The results showed that straw mulching, intercropping, chemical fertilizer could all improve the amount of the soil microbial biomass C. The annual variation of microbial biomass C showed the tendency of “low-high-low-high”, and the influences were variable with the time. For the annual average of soil microbial biomass C, Treatment 1(T1) (straw mulching + 100% organic manure), Treatment 2 (T2) (straw mulching + 75% organic manure + 25% fertilizer), Treatment 3 (T3) (straw mulching + 50% organic manure + 50% fertilizer), Treatment 4 (T4) (straw mulching + 25% organic manure + 75% fertilizer), Treatment 5 (T5) (100% fertilizer),Treatment 6 (T6) (intercropping white clover) were 17.05%, 32.38%, 32.05%, 24.30%, 26.23%, 24.63% higher, respectively, than CK, and the differences among all the treatments were significant (P < 0.05). The correlation of the SMBC with the active organic matter, the total nitrogen, the microbial biomass N, the microbial biomass P were remarkable, but no significant correlation was found with available nitrogen, total phosphorus, total potassium and moisture. Compared with other treatments, those mixed with organic matter and chemical fertilizer were more advantageous to enhance the soil fertility.

The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE SYNTHASE (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.

Background High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). Results We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. Conclusion By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.

High throughput biological experiments produce a large amount of biological data that can be updated by time. Inconsistent data stored in the same or different databases may lead to serious biological research problems. Constraint management is important to ensure biological data integrity. Some existing databases were built for the easy use for biologists; however the database management system (DBMS) may not have a sufficient constraint management system. In this paper, we propose an XML-based active rule language, named BioRL, to enforce constraints on existing databases without changing the original system structures or the underlying databases. In BioRL language, biological semantics are represented declaratively in active rules by using XQuery expressions and functions. This paper presents the syntax of the BioRL language, with examples that illustrate the use of BioRL in an application environment. This paper also presents the BioRule system to support the specification and execution of BioRL, focusing on the architectural components of the BioRL parser and the BioRL repository.

XML is becoming one of the most common means to exchange data throughout the internet. Biological research is advancing at very high rates as a result of the large amounts of information that can be passed to researchers throughout the world, thereby increasing collaboration and reducing redundancy. There are limitations to the use of this data if there is no ability to verify it. This paper presents our BioRule system that uses active rules to verify the integrity of XML data. This system consists of a language named BioRL and an execution environment that supports event detection and rule processing. The paper discusses the language, architecture, and implementation to enforce constraints over XML documents being manipulated within a native XML database.

Constraints are important to ensure consistency and validity of biological data to computerize biological findings. Incorrect data could lead to serious scientific problems when conducting further biology research and experiments. We propose an XML-based active rule system named BioRule to enforce constraints on top of existing data sources. The BioRule system serves as a middleware to filter inconsistent data before populating or updating data sources. Biological semantics are specified in active rules, while the validation can be enforced by the BioRule system automatically according to the defined rules. To facilitate and simplify the specification of active rules, we developed a web-based user-friendly tool to guide end-users. Rule examples, over an existing biology application, are also provided in this paper to illustrate the specification of active rules though web-based interfaces for constraint validation.